Tau'ri-Wraith skirmishes

This is a list of skirmishes that have occurred in the Pegasus galaxy between the Tau'ri and Wraith during the Tau'ri-Wraith war.

Rescue of the Athosians and Atlantis personnel
After figuring out the Stargate address of the Wraith homeworld and finding the Puddle Jumper Bay, Major John Sheppard leads a rescue team to find Colonel Marshall Sumner, the other Atlantis personnel and the captured Athosians. Arriving in orbit through the Stargate located there, Sheppard manages to locate the Hive Ship on the surface and lands getting a Life signs detector from the Jumper to use to find the prisoners. Leaving everyone else behind and ordering them to set up C-4 around the hive, he and Lt. Aiden Ford enter it to rescue their people. Finding the captured people, Sheppard sets up C-4 to blow the door when the rest of the C-4 is blown and orders Ford to fall back as he goes to find Summner who is being interrogated by the Wraith Keeper. He finds Sumner being drained of his lifeforce as an interrogation technique and repeatedly tries to kill the Keeper, but due to her feeding, she manages to heal herself each time. Seeing Sumner severely drained of life and near death, Sheppard kills him in a mercy killing but is caught by other Wraith soon thereafter. The Keeper interrogates him, but before she can feed on him, Ford returns and kills the two Wraith warriors guarding him, freeing Sheppard. Sheppard orders the C-4 detonated, freeing the prisoners and killing all of the other awake Wraith around the hive, and then stabs the end of a Wraith spear gun through the Keeper's chest, mortally wounding her. Before she dies, she warns Sheppard that his actions in killing her will cause all of the Wraith in existence to wake up which they start to do as Sheppard and Ford watch. Fleeing back to the Jumper, they come under attack by Wraith Darts, but Sheppard manages to drive one off before it can cull them and they make it to the Jumper only to find the Stargate guarded by a bunch of Darts. Sheppard decloaks and leads the Darts away from the Stargate but is unable to recloak due to damage. He manages to take out a couple of Darts as they dial the Gate and send the IDC, and the rest follow him through the Stargate to Atlantis but are destroyed by Atlantis' Stargate shield.

Second encounter on the Wraith homeworld
Major John Sheppard and his team travel back to the Wraith homeworld to gather intelligence on the Wraith. There they find the Hive Ship they were in earlier gone. Unfortunately they come under attack by Wraith warriors that were apparently left behind and while escaping the Puddle Jumper is damaged. Also an Iratus bug attaches itself to Sheppard's neck. The Jumper manages to escape into orbit, but gets stuck in the Stargate. After many attempts the Iratus bug is removed by using a Defibrillator to stop Sheppard's heart, causing the bug to think he's dead and let go. Ford shoots and apparently kills it afterwards. Finally the team manages to retract the drive pods and opens the back hatch to use the decompression to return through the Stargate. As this is done the Iratus bug revives, but is blown out into space and is presumably killed by the vacuum of space.

The capture of Steve
Using the Wraith relay device in Teyla Emmagan's necklace, the team sets a trap in order to catch a Wraith. A Wraith Commander later known as Steve and three Wraith warriors arrive following the tracking signal from the necklace and a short battle ensues. One is killed by claymores and Teyla and Lt. Aiden Ford gun down another one. Teyla goes after Steve while Major John Sheppard and Dr. Rodney McKay manage to down the last Wraith first with gunfire and then when it gets back up with tazers. The Wraith self-destructs however to prevent capture. Teyla goes one on one with Steve and loses and is about to be fed upon by him when Sheppard shoots him with a Wraith stunner rifle. Steve goes to self-destruct, but is stopped by Sheppard and taken captive.

Tau'ri-Genii infiltration of a Hive ship
As part of their plan to get information in order to nuke all of the Hive Ships in the galaxy, a combined team of Tau'ri and Genii soldiers take a Puddle Jumper to a landed hive ship that has not yet fully awakened from hibernation. There they take a Wraith data storage device to get the information they need on the Hive Ships and Teyla tries to free cocooned humans, but the Genii soldier Tyrus kills one that awakens and alerts the Wraith to their presence on the Hive Ship. Teyla tries to save Tyrus, but he is stunned and captured by Wraith guards and she is forced to leave him behind. The combined team escapes with the information they need and no further casualties, but the Tau'ri learn from the data that there are at least 60 Hive Ships in the Pegasus Galaxy, possibly more.

Skirmish of the Light Bugs Planet
Major John Sheppard, Dr. Rodney McKay, Dr. Abrams and Dr. Brendan Gall go to check out an Lantean defense satellite near the orbit of the second planet in the Lantean system. There they detect a signal and land on the planet. Checking out the signal they find a crashed Wraith supply ship, apparently shot down during the siege by the defense satellite. Exploring, they find that all of the humans being transported are dead and so appear to be the crew. Unfortunately it turns out that there is one Wraith survivor. He survived by feeding on the humans being transported and his own crew. He feeds on Abrams to death and feeds on Gall until he's very weak. The Wraith then goes to the Puddle Jumper landed nearby, but as the Jumper requires the ATA gene to operate, he is unable to fly it. Sheppard lures him away from the Jumper but he puts up some kind of shield that prevents entry into it. Despite all of Sheppard's best efforts to kill him, he survives each attempt due to having fed recently and Sheppard's weapons are damaged and he is injured. McKay wants to help but due to helping Gall is unable to. Gall tries to convince him to go, but when he can't kills himself. McKay arrives to help Sheppard and unloads two pistol clips into the Wraith to little effect. Another Jumper arrives to help and using a power bar, Sheppard gets the Light bugs to gather around the Wraith. He has the Puddle Jumper lock onto the Wraith's lifesign (which is the strongest due to the light bugs swarming around him) from orbit and fires a Drone weapon into him. The drone destroys and kills the Wraith, ending the battle.

Wraith attack on Proculus
While Chaya Sar is away at Atlantis and not protecting the planet Proculus, the Wraith attack with two cruisers and hundreds of Wraith Darts through the Stargate. Chaya returns and Major John Sheppard takes a Puddle Jumper to help as best as he can. He manages to destroy a few Darts before Chaya appears to him and tells him to leave the rest to her. She uses her powers to release a massive electromagnetic blast and destroys the Wraith Darts and cruisers, ending the attack.

Skirmish 50 light years from Lantea
In an attempt to stop the second wave of Hive Ships from reaching Atlantis, the Daedalus travels to where they are making a hyperspace pit stop 50 light years away. Once there they wait for the fleet to arrive and manage to beam Nuclear warheads into two of the Hive Ships, destroying them. Unfortunately the Wraith manage to employ countermeasures and block any further transport and a short battle ensues. After taking some damage and having two Wraith cruisers get over the top of the Daedalus in an attempt to board the ship, the Daedalus makes a jump to hyperspace, escaping. Its later revealed that at some point during this engagement the Wraith downloaded a computer virus into the ship's computers that later try to take over the ship and bring it to the Wraith before finally being destroyed.

The scooping of McKay and Cadman
While on the planet Thenora that was recently destroyed by the Wraith, a Wraith Dart attacks. It manages to cull Dr. Rodney McKay and Lt. Laura Cadman and heads for the Stargate to return to its Hive Ship. Lt. Colonel John Sheppard manages to shoot it down with a M249 Squad Automatic Weapon before it can escape and Dr. Carson Beckett finds the pilot injured, but alive. Beckett goes to help him, but seeing that the pilot is reaching for the Dart's self-destruct, Sheppard kills him. McKay is retrieved from the Dart at the scene but Cadman's mind gets trapped inside him. Later McKay and Cadman are separated and Cadman's body is beamed out of the Dart's storage device.

Death of the Daimos
A Wraith scout ship crashed on a planet years ago with the survivors being found by nearby villagers. The villagers, unsure of what they'd found, killed the survivors and burned the bodies, but two Wraith survived: a female infant later named Ellia and an adult male referred to by the villagers as the Daimos. The Daimos fed on the humans of the planet in order to survive a few times a year and Ellia was raised by a man named Zaddik who found her and didn't want her to be killed. She eventually lost the ability to eat normal food and fed on him a few times at his own insistence making him look much older than he really was. Zaddik started making a serum out of Ferassin root to suppress her hunger, but what she didn't have the heart to tell him was that it didn't work and she fed on the villagers too, timing it so that her feedings coincided with that of the Daimos. Lt. Colonel John Sheppard and his team arrive on the planet and learning of the Daimos decide to hunt and kill it. They meet Ellia and bring in Dr. Carson Beckett to examine Zaddik's serum and he brings with him an experimental retrovirus created to turn Wraith into humans. Desperate, Ellia takes it but it works the opposite way and turns her more bug than human. Dr. Rodney McKay and Beckett end up facing the Daimos, but before it can kill them, Ellia arrives, fights it and snaps its neck, killing it. Acting purely on instinct now, she injures Teyla Emmagan somewhat and fatally injures Zaddik who later dies of his injures after reuniting with his estranged father who believed him dead. Sheppard and Ronon Dex face Ellia and she tries to feed on Sheppard but fails and is killed by the two. It is later revealed that her attempt to feed on Sheppard infected him with the retrovirus, but Beckett manages to later find a cure.

Skirmish of Aurora
After the ZPM is installed in Atlantis, the city sends out a beacon to all ships instructing them to return to the city immediately. The Aurora receives the signal and becomes active making it appear on Atlantis' Long range sensors. As its no where near a Stargate, the Daedalus is dispatched to investigate it. Unfortunately the awakening of the Aurora alerts the Wraith to its presence and they dispatch a Wraith scout ship to investigate. A Wraith boards the ship, kills the First Officer, Trebal, and enters the VR program after messing with it to trick the crew into revealing how to upgrade hyperdrives from interstellar to intergalactic in order for the Wraith to be able to reach Earth. The Daedalus arrives and destroys the scout ship and Lt. Colonel John Sheppard and his team board the Aurora. Sheppard enters the VR and the Wraith does its best to prevent Sheppard and the Captain of Aurora from talking so Sheppard won't reveal the truth to him. Dr. Rodney McKay finds the Wraith and after freeing Sheppard in the VR and finding out that a message containing the Wraith's weakness has been deleted, he tries to disconnect the Wraith from the system while in the VR Sheppard tries to convince the Aurora's Captain of the truth. McKay manages to disconnect the Wraith and as it disconnects, in the VR it shifts partially into its true appearance which convinces the Captain. The Wraith wakes up and McKay runs while shooting at it. In the VR Sheppard explains the situation to the Captain along with the fact that the Daedalus detected two Wraith cruisers on the way, and the Captain, knowing the crew is beyond help but wanting to help still, gives Sheppard the Aurora 's self-destruct code explaining that the blast will be enough to destroy the cruisers. Sheppard exists the VR in time to kill the Wraith with his pistol. After setting the self-destruct, Sheppard and McKay beam back to the Daedalus just before the cruisers arrive and the Daedalus moves out of the way just in time before the Aurora explodes, destroying the two cruisers.

Skirmish on the Wraith outpost
Michael Kenmore, a Wraith Commander (and scientist as its later revealed) who has been turned human, starts to revert back and kidnaps Teyla Emmagan and travels to a planet full of Wraith that he remembers the address of. Once there he and Teyla find a Hive Ship landed on the ground along with thousands of Wraith. Michael has reverted back enough by this time that he can feed again and he threatens to feed on Teyla. Teyla tells him to go ahead, but as he still cares about Teyla, he fights with himself for a moment before going to feed on her. Lt. Colonel John Sheppard, Dr. Rodney McKay and Ronon Dex arrive having gotten the address from a piece of rock Teyla inscribed it upon, and Sheppard shoots Michael. Taking Teyla with them they run for the Stargate and escape as the other Wraith find Michael who is still alive.

Skirmish over M8G-352
Lt. Colonel John Sheppard and his team arrive over M8G-352 in the Hive Ship they captured in the Battle of the Void. They take a Puddle Jumper to the surface and rescue Dr. Carson Beckett, but its too late for the rest of the humans. Dr. Rodney McKay tries to detonate the Mark IX Sheppard left behind, but it doesn't go off as Michael Kenmore has managed to disable it. Sheppard orders McKay to fire on the planet in an attempt to take out the camp and the human-form Wraith there, but another Hive Ship arrives and starts firing at them. They are unable to fight back, but continue firing at the planet in an attempt to kill all of the human-form Wraith anyway. Ultimately they lose power and are about to be destroyed. Later when the Daedalus arrives to help, all it finds is the debris field from the team's destroyed Hive Ship and no sign of survivors or the other Hive Ship. Then the team contacts them: they managed to escape the ship's destruction in the Puddle Jumper and are grateful the Daedalus came as they had no other way of getting home as the planet has no Stargate. They believe that all of the human-form Wraith were killed by the bombardment, but its later revealed that Michael at least managed to survive but it is unknown if any of the others did.

Ronon's capture on Sateda
A village of people who were culled due to Ronon Dex accidentally leading the Wraith to them when he was a Runner captures the team and summons the Wraith who have promised to leave the village alone if Ronon is turned over to them. Ronon manages to convince the villagers to let the rest of the team go, but by the time they get back with a rescue, the Wraith have culled the village and taken Ronon to the Hive Ship where he encounters the Wraith Leader responsible for the destruction of his homeworld. The Wraith Leader has him implanted with another Wraith tracker and set loose on the surface of Sateda in order to hunt him. In order to make sure he can't get away, the Hive Ship destroys Sateda's Stargate with a blast from orbit. On Atlantis, Dr. Rodney McKay manages to track down his tracking device and Lt. Colonel John Sheppard, McKay, Teyla Emmagan and Dr. Carson Beckett take the Daedalus close enough to Sateda to travel by Puddle Jumper down to the surface to help. Ronon encounters increasing numbers of Wraith coming after him and wins each time, but is injured and outnumbered as there are 25 coming after him now. Sheppard and Teyla show up to help and he insists on killing all of the Wraith as he feels that it will draw the Wraith Leader himself to the surface so Ronon can fight and kill him for revenge. Together the three kill all of the Wraith while McKay and Beckett both fight over a gun on the Jumper, both wanting to come and help but being unable to resolve the argument before the fight is over. With the death of these Wraith, Ronon successfully lures the King to Sateda's surface for a fight and warns Sheppard and Teyla not to get involved unless he (Ronon) is killed, threatening them with death if they interfere in the fight. Ronon and the King go hand to hand but in Ronon's weakened state he is no match for the King who goes to feed on him. Both are surprised however, when the Puddle Jumper piloted by McKay decloaks nearby. Unable to take watching the fight anymore, he and Beckett decided to intervene and Beckett kills the Wraith Leader with a drone fired from the Jumper. The team barley escapes as the Hive Ship fires at them, but once they get to space Ronon thanks and hugs Beckett for killing the Wraith and Beckett removes the tracking device from his back and they return to the Daedalus and Atlantis.

Skirmish of the Mobile drilling platform
Lt. Colonel John Sheppard, his team, Dr. Elizabeth Weir and a team of scientists head to a Mobile drilling platform that they learned the existence of and location of from Atlantis' database. Once there they get to work on setting it up, but Teyla senses a Wraith presence nearby. She tries to connect with the mind of the Wraith, but after she wakes up claims she was wrong and that there was no Wraith nearby. But it is revealed that she is under the control of the Wraith in question and she sabotages the drilling platform's systems before being released from the Wraith's control. Meanwhile the Wraith arrives and it is revealed that it is in fact a Queen. She tries to fly the Puddle Jumper, but can't as she doesn't posses the ATA gene and she feeds on one of the scientists that comes to the Jumper but first forces him to call Sheppard. When Sheppard arrives she tries to force him to fly the Jumper, but Ronon Dex takes a shot at her and misses, hitting the Jumper's window and blasting it out, releasing ocean water into the drilling platform. McKay activates the emergency force fields to prevent the water from getting too far into the base, but the force of the water knocks out Sheppard, Ronon and the queen who they capture after waking up. The queen won't tell them anything beyond "you are all going to die" so Teyla connects with her mind again and finds out her past: she was the queen of a great alliance of Wraith who led the first wave of the attack on Atlantis during the siege 10,000 years before. Her Wraith cruiser was shot down but survived intact on the ocean floor of Lantea for 10,000 years with the queen surviving by feeding on her own crew until she was all that was left of it and went into hibernation waiting for a rescue that would never come. She woke up once she sensed Teyla's presence and swam over underwater as it wasn't far and tried to take the Puddle Jumper, but needed Sheppard to fly it. Teyla learns that before she left the cruiser, she set the self-destruct which would cause an eruption as they are on thin crust which would destroy both the drilling platform and Atlantis. Sheppard and McKay take two Ancient pressure suits and walk underwater to the cruiser where they attempt to deactivate the self-destruct but discover that they need a command code. Teyla decides to connect with her mind in an attempt to get the command code, but the queen gains control and forces Teyla to release her, but before she can feed on her she reads Teyla's mind and discovers Sheppard and McKay were able to fix the cruiser and plan to fly it to the mainland so it can detonate safely. She leaves Teyla alone and swims back to her cruiser where she confirms with Sheppard that it can fly than deactivates the self-destruct. As she goes to feed on him, McKay empties a P90 into her back, weakening her but not killing her. She turns on him but Sheppard unloads his pistol into her back finishing her off. With her death Teyla can no longer sense the Wraith meaning she was the only one. Its revealed that Teyla tricked the Wraith Queen into believing that the ship had been repaired in order to get her to deactivate the self-destruct which then allowed McKay and Sheppard to kill her. They manage to get the radio back online and contact Atlantis who sends a rescue Jumper.

Skirmish of Michael's Bug People
Lt. Colonel John Sheppard's team is sent to investigate why Atlantis has lost contact with the Taranian settlement. Exploring they find a hatched cocoon and finally the Taranian's who have been fed upon by Iratus bugs. They find what looks to be a Wraith lab and come under attack from one of the Bug People who they manage to drive off. On the surface Lt. Negley and his team are captured when a Wraith Dart suddenly arrives and Negley is apparently forced by whoever was in the Dart to send a message to Atlantis saying that the Taranians simply moved to another settlement further away. In the tunnels below the surface, Sheppard, Dr. Rodney McKay, Ronon Dex and Teyla Emmagan find hundreds of cocoons filled with Bug People. They set C-4, but barley get away before one of the Bug People hatch. Sheppard sets off the C-4 destroying the cocoons and hatched Bug Person. They retreat to the Stargate but are unable to dial out as the person responsible for these creatures has removed the control crystal. After returning to the tunnels to search for Negley and his team, Sheppard and his team come under attack from a Bug Person and are separated from Teyla. This time the Bug Person is killed but Teyla is captured by the person responsible for the creation of them: Michael Kenmore, the Wraith turned human a couple of times who was believed to have been killed on M8G-352. Michael explains that he was rescued by the Hive Ship that arrived, but they sensed that he wasn't fully Wraith and he was forced to run for his life. As he was wanted dead by both human and Wraith, he decided to reverse the Iratus bug retrovirus used to turn him human and create a creature even more powerful than Wraith or human by having Iratus bugs feed on humans and then lay eggs while they still had a lot of human DNA left in them from the feeding which he then manipulated to create the Bug People to do his bidding. Sheppard, McKay and Ronon blast there way through a sealed door to a shielded part of the complex where Teyla is held as Michael releases an Iratus bug to feed on Teyla and continue his experiment. The three find the dead bodies of the marines and are attacked by another Bug Person who Ronon manages to kill. They manage to reach Michael's lab just before the Iratus bug can feed on Teyla and Ronon kills it and they free Teyla who reveals that Michael is behind everything. Sheppard and Ronon go after Michael while Teyla and McKay stay to examine the data in his computers and McKay attempts to unshield the base. McKay manages to unshield the base as Michael releases his Bug People. Ronon ends up going up against a few as Sheppard and Michael confront each other. Sheppard tries to get him to give up the DHD control crystals but he refuses and runs off when Sheppard comes under attack from more Bug People which Ronon rescues him from while McKay and Teyla head for the Stargate. Ronon and Sheppard escape through an air shaft and find Michael's Wraith Dart which Sheppard steals and scoops Ronon up with the culling beam. McKay and Teyla get surrounded by the creatures and stunned by Michael, but before any more can happen to them, Sheppard beams them aboard the Dart and they escape through the Stargate to another planet using the Dart's DHD. There they ditch the Dart and return to Atlantis where they dispatch the Daedalus to deal with Michael, but he has already left by the time the ship gets there. From the information McKay downloaded from Michael's computer they learn that his number of Bug People is well into the hundreds and he had labs on three more planets other than the one the Taranians settled on. Also he got the location of that world from the information the Wraith had downloaded during their brief disastrous alliance with them that had nearly led to the Wraith coming to Earth.

Skirmish of the Wraith Lab
Lt. Colonel John Sheppard's team teams up with Ronon Dex's old friends from Sateda Tyre, Rakai and Ara to attack a Wraith weapons research facility. Initally they are reluctant as the Wraith are at war with the Asurans, but agree after learning that one of the things that the lab is studying is a way to shut off the Asurans attack command. The two groups head there via Puddle Jumper, but Sheppard, Dr. Rodney McKay and Teyla Emmagan are captured when the others betray them as they are really Wraith worshippers having been driven insane by repeated feedings and restorations of life. The Wraith want McKay to figure out how to deactivate the attack command as he was the one that reactivated it in the first place and the changes he'd made to the Asuran base code had made their deactivation virus that they had used the first time, useless. They planned to force McKay to change it so that it would work and upload it through a captured Asuran. Ronon managed to escape through the Stargate and brought back a rescue team lead by Colonel Samantha Carter which distracted the Wraith Darts guarding the lab by drawing them off with a Puddle Jumper. The rescue team frees Sheppard and Teyla and frees McKay just as the captured Asuran escapes due to power fluctuations caused by the rescue. The Asuran ignores them and runs off and presumably follows the Wraith attack command and kills the remaining Wraith in the lab. The Wraith Commander is caught by Ronon, but his friends arrive and the Commander leaves them to deal with Ronon. Ronon fights them in hand to hand combat and Rakai accidentally kills Ara after which Ronon kills him. Ronon lets Tyre go saying that there had been enough death that day. He then returns to his true friends: Sheppard, McKay, Teyla, Carter and the rest of the Atlantis expedition who he'd been prepared to leave to rejoin his friends from Sateda.

Wraith attack on the Travelers' Aurora ship
After Lt. Colonel John Sheppard manages to take control of the Traveler Aurora-class battleship, he tries to take it to Atlantis but is forced to stop and drops it out of hyperspace in a solar system with a Stargate and sends out an SOS in morse code. Atlantis receives it, but unfortunately so do the Wraith. The Wraith send a Wraith cruiser to attack the ship. Sheppard manages to convince Larrin to let him go to help. He makes his way to the ship's Drone weapon Control chair, but due to a malfunction of some kind is unable to fire right away. Meanwhile, the cruiser opens fire on the ship and as the shields are only at twenty percent, they fail and the cruiser takes out the bridge, killing the two Silas and Nevik. Sheppard manages to fix the problem and fires a salvo of drones, destroying the cruiser, but four Wraith Darts escape the destruction and land in one of the ship's bays. One of the Wraith attacks Larrin, but Sheppard kills him. Larrin then leads two more into a corridor on the side of the ship and Sheppard fires a drone into it, releasing the Wraith into space and killing them. Unfortunately, the last Wraith had broken off before this attack and ambushes Larrin and drains her lifeforce somewhat in order to question her but is in turn ambushed by Sheppard who bluffs him with an empty gun into restoring her lifeforce. Afterwards he lets the Wraith escape via its Dart and the Stargate in the solar system as part of the deal.

Skirmish of the Wraith cloning facility
Todd steals three ZPM's during the Battle of Asuras and decides to use them to clone himself a new army of Wraith at the Wraith cloning facility in order to wipe out the other Wraith and create an army completely loyal to him. He is betrayed to another Hive Ship by one of his men and his ship is attacked, his crew is killed and he is taken prisoner. Before he's taken prisoner he activates his subspace tracking device before its cut out of him, leading Sheppard and his team to his damaged and abandoned Hive Ship which they take for their own. After learning of the cloning facility, Teyla Emmagan flies the Hive Ship there to check it out as while they don't know what it is, they learn that it was crucial to the Wraiths defeat of the Ancients. They arrive in orbit of one of the planets and Lt. Colonel John Sheppard, [Dr.]] Rodney McKay and Ronon Dex take a Puddle Jumper down to the facility while Teyla, Major Evan Lorne and his team remain behind on the Hive Ship. Once there they find Wraith warriors being cloned and many cloning pods as well as a Queen. Not understanding what's going on, they rescue Todd who explains it to them and how the facility was instrumental in their defeat of the Ancients: they defeated the Ancients through sheer numbers which were formed through this cloning facility. They couldn't use it in their war with the Asurans as it required ZPMs to work, but he'd gotten those during the last battle. The team and Todd get ambushed by the Wraith on their way out and while Todd does escape, the team is captured. Todd takes a Dart and makes his way to the Hive Ship and tries to convince everyone else to leave, but Teyla refuses saying she's got another idea of how to save their friends. In the facility the Queen interrogates Sheppard and prepares to feed on him when Teyla takes control of her and forces her to have the other Wraith send them back to a cell. While Teyla mentally fights the Queen, she forces her to go and release the rest of the team, but the Queen goes after her baby. At Teyla's urging, Sheppard kills the Queen saving Teyla and her baby. In orbit of the moon the Queen's Hive Ship locates Atlantis' and attacks and Todd tries to hold them off as long as possible to allow Sheppard, McKay and Ronon time to get back to the ship. The three manage to fight their way out having no time to disconnect the ZPMs as the cloning process has been started and make their way back to the hive ship in their Puddle Jumper. Needing to destroy the facility, Sheppard has Teyla set the hive ship on a collision course with the facility while the team and Lorne's team escape in the Puddle Jumper and Todd escapes in a Wraith Dart. They watch as the Hive Ship crashes into the facility, destroying it, and then escape through the planet's Stargate back to Atlantis.

Skirmish of Michael's facility
After learning of a possible location of Teyla Emmagan from Todd, the team takes the Daedalus to the given location where they beam into Michael's facility. There they encounter two guards while the Daedalus comes into battle with Michael's cruiser in orbit. The two guards are killed by Lt. Colonel John Sheppard and Ronon Dex and Sheppard learns that Teyla is likely on Michael's ship so he orders the Daedalus not to destroy it. Michael's cruiser is no match for the Daedalus and takes heavy damage so Michael runs. The Daedalus attempts to take out the hyperdrive with its Asgard plasma beam weapon, but misses and Michael gets away. The team investigates the facility and finds the clone of Dr. Carson Beckett there.

Firefight in Michael's base
The team learns the location of Michael's base where he is holding Teyla Emmagan from Nabel Golan and travel there by Stargate. There, after a brief fight with a few of Michael Kenmore's hybrids, the team finds and rescues the missing Athosians including Halling. Michael learns of their presence in his base and terminates his experiments and orders two of his hybrids to take Teyla to his cruiser which is parked nearby. Lt. Colonel John Sheppard, Ronon Dex and Dr. Rodney McKay come into conflict with three of Michael's human soldiers so Dr. Carson Beckett heads off to rescue Teyla alone and kills the two hybrids guarding her, but is stopped when Michael himself shows up and is unable to shoot him due to being susceptible to his influence. Beckett is stunned and Michael makes his way to his cruiser with Teyla. Meanwhile McKay, Ronon and Sheppard manage to gun down Michael's men, but by the time they find Beckett, Michael manages to escape again in his cruiser.

Skirmish of the Wraith lab
With the help of Tyre, a former Wraith worshipper, Lt. Colonel John Sheppard's team infiltrated a heavily guarded Wraith lab in order to save their captured comrade Ronon Dex. The team fought to the relay chamber where they planted C-4 explosives. They then went to the Wraith transporter and found Ronon, who had been turned to a Wraith worshipper. Tyre betrayed the team and he and Ronon took down the team together and locked them up in different cells. In turn Tyre later betrayed the Wraith commander and helped in freeing Sheppard, which ended in a sword fight between Tyre and Ronon. The rest of the Tau'ri forces suddenly arrived in the middle of the duel and Teyla Emmagan hits Ronon with a Wraith stunner. Under the threat from the C-4 detonations, the Wraith Commander allowed the Tau'ri to exit the lab. After the team had reached safety Tyre detonated the C-4, blowing up himself along with the Wraith and the lab.

Fight for the Balarians
Due to all survivors of the Hoffan drug being immune to feeding, the Wraith begin tracking down all survivors and killing them. They wipe out the Balarians homeworld and track the Balarians to another world that they relocate to with the help of the Atlantis expedition. A small group of Wraith arrives through the Stargate and offers the villagers a deal: hand over the Balarians and they'll leave the village alone, don't and they'll wipe out the village and all of the villagers. Teyla Emmagan and Ronon Dex plan to retake the Stargate, but more Wraith arrive from patrol so they are unable to do so. Jervis betrays the Balarians to the Wraith in an attempt to save himself and sends one group to the Wraith at the Stargate. Before he can send anymore he is stopped by Dr. Carson Beckett who manages to convince him to stop. In an attempt to save himself, Sefaris betrays Beckett to the Wraith and Beckett and Dr. Rodney McKay are captured by them and taken to the Hive Ship which arrives in orbit. There, the Wraith Commander forces Beckett to complete his now dead scientist's work on detecting plague survivors. On the surface in order to protect the Balarians, they are taken to a nearby mine for protection while Lt. Colonel John Sheppard, Ronon and Teyla try to come up with a plan to help them escape. Beckett completes the scientist's work and tests himself for the drug. Learning that he has it (Michael Kenmore likely gave it to him as a defense against the Wraith), he tricks the Commander into feeding on him, killing the Commander. He takes the Commander's stunner and frees McKay. The two make their way to a console where they use the ship's communications system to communicate with Sheppard who orders them to disable the Hive Ship's weapons as part of his plan. McKay does while Beckett covers him and then the two run off. On the planet's surface, Elson frees Jervis to make a deal with the Wraith and tells him where the remaining Balarians are located. On the Hive Ship McKay and Beckett make their way to the Dart Bay but are unable to fly a Wraith Dart and Wraith start to blast through the door into the Bay. Jervis leads most of the Wraith into the mine where they find the Balarians gone and a block of C-4 which Sheppard detonates, killing the Wraith and Jervis and his men. With most of the Wraith killed in the mine, they are easily able to take the Stargate and start to evacuate everyone to Atlantis. The Hive Ship tries to fire at them, but are unable to as McKay had disabled the weapons so the new Commander launches Darts to attack them. One tries to cull Teyla but instead deploys McKay and Beckett who beamed themselves into Dart storage and programed it to drop them off once they realized that the Darts were going to be launched. Everyone escapes through the Stargate and the Balarians and villagers are resettled on another planet.

Skirmish on the diseased Hive Ship
Todd's Hive Ship arrives in orbit of M35-117 and automatically sends a video message to Atlantis for help. Todd and his crew have taken Dr. Jennifer Keller's gene therapy but it has left them with a disease so they set course for Atlantis and went into stasis hoping the people of Atlantis could find a cure. On board the team finds power fluctuations, walls melting and appearing and Wraith warriors attacking them as the power fluctuations have triggered a safety protocol that causes the pods to open. After reviving Todd they discover that the disease has infected the Hive Ship itself as well. Dr. Rodney McKay shuts down most of the pods, killing those Wraith, but not before a couple of dozen are released. The three teams, excluding McKay and Keller go after those Wraith, but the ship starts to break apart. The teams manage to get to the forward section and McKay seals the bulkheads before the ship breaks in half, killing the Wraith in the rear section and leaving Todd as the only Wraith still left alive. He manages to land the front half of the Hive Ship on the planet's ocean using the Maneuvering thrusters and they are rescued by teams from Atlantis before the Hive Ship sinks. Todd is later released to seek a dangerous cure that he is aware of which leaves him grateful to the Atlantis expedition.

Skirmish over the alternate Earth
In an alternate reality, a Hive Ship somehow finds and reaches Earth and launches an attack. A battle ensues between Wraith Darts and Earth's F-302s. In the battle, there are losses on both sides, but it ends with Drone weapons fired from the Ancient Control chair in Area 51, destroying the Hive Ship and all but one Dart that manages to survive, albeit damaged. The Dart crashes on Earth and the Wraith pilot starts building a transmitter using materials from its Dart and Earth materials in order to send a message to lead the other Wraith to Earth. The Wraith also feeds on many people and becomes a serial killer while successfully hiding as a human.

Skirimish in the desert
Detective John Sheppard manages to locate the Wraith survivor and tries to sneak up on him as he activates his transmitter. The Wraith hears his car and engages in a gunfight with Sheppard, apparently mortally wounding him. Sheppard shoots the Wraith several times to no effect. He runs out of ammo and the Wraith prepares to feed on him. Before the Wraith can succeed, a pair of A-10 Thunderbolt IIs, dispatched to take him out, arrive. The Wraith activates his transmitter and sends his message, but before it can be sent out for long, the Thunderbolts destroy the trailer, killing the Wraith and destroying his transmitter. Sheppard apparently dies of his wounds and Dr. Rodney McKay discovers that while the message didn't reach the Pegasus Galaxy, it got sent through to other realities and would be stronger there, meaning that other realities out there had the threat of the Wraith receiving the message and coming to Earth. This leads to the Battle of the ZPM powered Hive Ship in another reality where a Hive Ship did receive the message and attacked Earth before being destroyed by the Lt. Colonel John Sheppard of that reality with a Nuclear warhead from the inside.