Standoff on the Genii homeworldEdit
After the mission to the Wraith Hive ship resulted in the death of Tyrus, Cowen double-crossed Major John Sheppard and his team, having his men surround them to get answers about Tyrus' death and to force them to hand over their weapons, Puddle Jumper and all of the C-4 they had on them while also keeping the Wraith data storage device with all of the intel. However, Sheppard had anticipated a double-cross and planned one of his own: he had two cloaked Jumpers nearby, ready to act on his order, Sheppard having told Cowen there was only one Jumper. Sheppard ordered the two Jumpers to decloak and ordered Cowen to order his men to stand down and let them go. Cowen initially hesitated, not wanting Sheppard and his people to get away, but after Sheppard ordered the Jumpers to prepare to fire, Cowen gave in and ordered his men to stand down though he wasn't happy about it. He also wasn't happy that Sheppard took the Wraith data device from him, basically telling him that by doing this he was making an enemy of the Genii which Sheppard wasn't worried about. (SGA: "Underground")
Skirmish on DaganEdit
After receiving a list of Stargate addresses where there should be Zero Point Modules from an alternate Dr. Elizabeth Weir, Major John Sheppard's team searched the planet Dagan which was on the list. Dagan proved to be the most promising because of the legend of the Potentia which was revealed to have been a ZPM. With the help of Allina and Sanir the team searched for and found eight of the nine Brotherhood Stones to the location of the ZPM, but Sanir was really a Genii spy who alerted the Genii to what they were up to. Commander Acastus Kolya, after being kicked out of Cowen's inner circle for failing in the Genii invasion of Atlantis, saw getting the ZPM as a way to deprive the expedition of more power and to redeem himself in the eyes of Cowen. He also saw it as a chance to get revenge on Sheppard who had shot him in the shoulder during their last encounter, a wound that still gave him pain. Koyla led a team of six men, including himself to Dagan where he had one of his men dart Lt. Aiden Ford unconscious while the rest of the team were in the chamber where the ZPM was. When Koyla and his men approached, Ford revealed he was faking unconsciousness and killed one of the Genii soldiers and took Tathal hostage before being overpowered. Sheppard and his team were shocked to hear Koyla's voice, having believed him to be dead, and were shocked and angered by Sanir's treachery.
Koyla ended up making a deal with the team: Dr. Rodney McKay finds the ZPM and he gets it and they get to go free, but he leaves everyone but McKay, Allina and Sanir trapped in the chamber without weapons or radios while he, his men and those three go check out the planet that McKay believes the last stone to be on. Three of the Genii are left to guard the chamber while Koyla, Pranos, McKay and Allina search for the last stone. They discover the Stargate address doesn't work, but McKay finds the last stone in the monastery's mural and the four return to the chamber where Sheppard, Ford and Teyla Emmagan have set a trap using a hidden knife Teyla possessed and two Stun grenades belonging to Ford. At the chamber, Pranos is killed when he tries to activate the stones in the wrong order, but Sheppard is able to figure out the right order and gets the ZPM. Taking advantage of the fact that Koyla is distracted, Ford detonates his grenades, stunning the Genii, Allina and McKay who are unaware of what is going on. Teyla kills two with her knife while Sheppard fights Koyla, eventually overpowering him and getting his FN P90 Personal Defense Weapon back from him while Ford overpowers the last Genii soldier and holds him with his own gun. Having defeated Koyla and his men, McKay retrieves the ZPM while Koyla tells Sheppard he should kill him. Sheppard chooses not to, telling Koyla he expects points with him for that next time, but swears to kill him if he ever does anything against them again. Sheppard promises to send a villager back to get Koyla and his remaining man in awhile before leaving the two in the chamber to be later retrieved. Unfortunately, even after Koyla is defeated, Sheppard and his team still don't get the ZPM as the villagers take it away from them to be hidden again as they are not Ancients. (SGA: "The Brotherhood")
Ladon Radim's coupEdit
After Cowen starts planning to use his Genii A-bombs to take over the galaxy, Ladon Radim plans a Coup d'etat against him and uses the Atlantis expedition as part of his plans. He sets a trap for the expedition using a dead Zero Point Module to lure them in. Meanwhile, the Genii set bounties for expedition members that have the Ancient Technology Activation gene and Major Evan Lorne and his team are captured. Ladon's supposed plan is to use them to make a gene therapy that would allow the Genii to fly the Puddle Jumpers. He supposedly was going to lure as many people to M6R-867, a dead world destroyed by the Wraith as possible to use as hostages in exchange for the Puddle Jumpers while sending terminally ill patients to Atlantis expecting they'd try to take hostages of their own. In reality he was doing this to lure Cowen and his elite personal guard into one location so he could destroy them with a nuke. He planned to let the expedition members die in the nuclear explosion as well, but after hearing that Dr. Carson Beckett could cure most of the patients including his sister, he decided to let the teams go. Ladon, his men, Lt. Colonel John Sheppard, his team, Lorne and his team escaped through the Stargate to Atlantis just before the nuke went off, vaporizing Cowen and his elite guard and leaving Ladon as the new leader of the Genii. After the death of Cowen and his guard, no one opposed his new leadership on the Genii homeworld so no one died there during the coup. (SGA: "Coup D'etat")
Acastus Kolya's capture of John SheppardEdit
Acastus Kolya, angry that Ladon Radim had betrayed his own plan to lead a coup to Cowen, leading to his exile, uses a spy in Radim's inner circle to lure Lt. Colonel John Sheppard and his team into a trap and captures Sheppard. Koyla then takes him to a prison where he has a Wraith held captive as well. Koyla then contacts Atlantis and demands Ladon Radim in return for Sheppard. Dr. Elizabeth Weir refuses and Koyla has the Wraith feed on Sheppard, aging but not killing him. Koyla then gives Weir three hours to change her mind before he has Sheppard fed upon again. In the cells, Sheppard learns that the Wraith is in the cell next to him and is furious. Radim gives the expedition locations of Genii safehouses Koyla might have gone to, but it proves to be a dead-end. Weir again refuses to turn over Radim and again Koyla has some of Sheppard's life drained away before giving Weir a final three hours to decide to comply. In the cells, Sheppard tries to convince the Wraith to work with him to escape, but the Wraith has lost all hope and refuses to even believe that Sheppard's friends will rescue him. When the time is up, Weir again refuses to turn over Radim and Koyla orders the Wraith to finish Sheppard off, but the Wraith only drains him a bit more before asking if Koyla wants him to finish the job and Koyla decides not to, and gives Weir two hours this time. The Wraith reveals that he stopped himself, having been convinced to try an escape with Sheppard.
When the guards come to take them again, Sheppard and the Wraith overpower and kill them, with the Wraith feeding off one, but the Wraith is slightly wounded in the process. The two escape the facility, killing several guards along the way, but the Wraith ends up seriously wounded and can't heal without feeding. They make it outside and try to reach the Stargate, but the Wraith's wounds and Sheppard's advanced age leave both very weak although they discover from a stolen radio that Kolya is concentrating his forces around the Stargate (which neither knows where it is) rather than searching for them. At the same time, Radim conducts an investigation that finds the spy and he learns the location of Koyla's base which he gives to Weir so she can launch a rescue while preparing a full company of his own men to attack. Radim only asks that Koyla be left for him to which Weir replies "no promises" and basically indicates to Ronon Dex that he is to kill Koyla if he gets the chance.
The rescue team, in a Puddle Jumper flown by Dr. Rodney McKay and consisting of Sheppard's team, Dr. Carson Beckett and several marines fly to the planet where Koyla's men finally locate Sheppard and the Wraith. Knowing they are both too weak to fight, the Wraith drains Sheppard to the point of death, giving him the strength to fight the soldiers and drain them all, healing his wounds. While he appears to be about to drain Sheppard completely, the Wraith actually restores all of the life he took from Sheppard, a previously unknown Wraith ability and Sheppard's team finally finds him moments afterwards. Koyla, outmatched, escapes through the Stargate, but before he goes, Sheppard promises him over the radio that next time he will kill Koyla on sight. Sheppard stuns the Wraith and drops him off on a planet where he can be found by the other Wraith before returning home to Atlantis. (SGA: "Common Ground")
Skirmish on Lucius' second homeworldEdit
Having grown tired of Lucius Lavin, the band of mercenaries he hired to make him look good summon former Genii Commander Acastus Kolya to help. Kolya tortures Lucius and captures Lt. Colonel John Sheppard's team and Dr. Carson Beckett. Sheppard, who went to rescue Lucius, manages to escape, but finds the Stargate too heavily guarded. Kolya plans to trade the team for weapons to use in a coup against Ladon Radim, but plans to kill Sheppard first. Sheppard and Lucius convince the villagers to stand up for themselves and help, and when Kolya threatens the team, John turns himself in. Kolya has his men shoot Sheppard, but Sheppard was wearing Lucius' Personal shield emitter and is unaffected by the bullets. Unfortunately the shield's power source is depleted by this and Lucius' overuse of it and it stops working. Before Kolya can have Sheppard killed, he and his men are surrounded by Lucius and armed villagers and his men surrender. Sheppard offers Kolya the chance to surrender himself, but Kolya just chuckles. Kolya and Sheppard go for their guns in an impromptu duel but Sheppard is a faster draw and shoots Kolya in the heart, killing him. (SGA: "Irresponsible")
Skirmish on Harmony's planetEdit
During a mission to Harmony's planet, Lt. Colonel John Sheppard and Dr. Rodney McKay were asked to accompany the new queen Harmony to the Ruins of Larris. During the journey, they were attacked by the Genii Commander Toran and his men. They were hired by Harmony's sister Mardola to kill Harmony so she could become queen and restore the trade agreement that Harmony's mother had voided. Toran chased Sheppard and McKay to the Ruins and were killed by the Mini-drones there. (SGA: "Harmony")
Standoff on WlandEdit
Six months after departing Pegasus to stop an attack on Earth by the Wraith, Atlantis returns to find Queen Death in power amongst the Wraith and devastating all the worlds in her path. One of these planets is Wland where Doctors Carson Beckett and Jennifer Keller set up a clinic to help the population. However, while they are there, Genii forces arrive to lend aid led by Sora Tyrus. Not sure if the Genii are friendly or not, Beckett sends Keller to contact Atlantis for backup. When Sora finds Beckett, she begins a search for other Atlantis personnel, not believing that he is alone and begins searching his supplies. Sora eventually decides to take both Beckett and the supplies in direct disobedience to Ladon Radim's order to leave the Atlantis expedition alone if they are encountered.
At the Stargate, Keller finds a Genii soldier guarding it, but is able to distract the man and knock him out with a rock to the head. Keller then returns to Atlantis where she gets Lt. Colonel John Sheppard, Teyla Emmagan, Ronon Dex, Doctor Rodney McKay and a team of Marines to help deal with the Genii. Returning to the planet, they find the guard, who had a skull fracture from Keller's rock, missing and make their way to the compound where Keller leads Ronon and three Marines to a back entrance to the compound. Ronon and his men get into position to cover Sheppard's group, but are unable to rescue Beckett as he's being too closely guarded. Sheppard approaches openly through the front gate and demands the release of Beckett and his supplies, but Sora refuses. She then asks about Teyla who had gone elsewhere after learning of Sora's presence on the planet and demands an exchange of Beckett for Teyla. Sora holds a gun to Beckett's head and threatens his life if they don't turn over Teyla to her, but in doing so, emerges from cover. Not wanting to risk Beckett's life if he misses, Ronon shoots Sora with his blaster, stunning her. However, a few of Sora's men are left in too good of cover to easily reach and one grabs Beckett, making the stand-off continue. One of Sora's men offers to release Beckett if the team will allow the Genii to take the supplies and Sheppard reluctantly agrees. The Atlantis team is then able to safely make their way back to the Stargate and Atlantis.
Following their return to Atlantis, Richard Woolsey contacts Ladon and demands their supplies back. Having heard of Sora's actions and not wanting to antagonize Atlantis yet, Ladon returns all of the stolen supplies and has Sora stripped of her rank and arrested to stand trial for her actions. (SGA: "Legacy: Homecoming")