Battle of the Super-hive

"What you really need to know is that this hive is a work in progress. It has yet to reach its full potential, which means if you attack it now, you may be able to destroy it. But if you hesitate, it will be too late, and this hive will be unstoppable."

- Todd

The Battle of the ZPM powered Hive Ship was a battle between the Wraith, Kenny's, ZPM powered Hive Ship and the Tau'ri. The battle took place in the Pegasus and Milky Way galaxies, and over Earth in 2009.

Spoils of war
"I may have acquired a few more [ZPMs] than I let on...let's not get caught up in unnecessary details."

- Todd

At the Battle of Asuras, Todd was able to steal a number of Asuran Zero Point Modules before the planet was destroyed. He used some of them to power his massive cloning facility, and set his underling, Kenny, to work on devising a way to integrate the ZPMs into a Hive ship.

The retrofit took well over a year to complete due to the incompatibility between Ancient technology and the organic nature of a Hive Ship. However, when Kenny was finally able to make it work, he mutinied, chasing Todd from the Hive. Todd crash landed on an unknown planet with a Stargate and dialed Atlantis. He apprised the Expedition of the situation and was permitted back into the city, to yet again ally against the Wraith, though with his track record of duplicity, the Expedition remained suspicious, notably John Sheppard. He revealed that the ZPM powered hive ship was still in the process of upgrading its systems, and if the process is allowed to complete, the Hive would be unstoppable.

Alternate reality
"That transmission would've been stronger in any other reality exposed to the rift."

- An alternate Rodney McKay

In an alternate reality, after a failed attack on Earth, a single Wraith Dart entered Earth's atmosphere after witnessing his Hive's destruction. After crash landing, the Wraith inside was able to salvage parts from his craft and began building a communications device. After gathering other equipment and money, the Wraith completed his device, tapped into Las Vegas' power grid and set to send his transmission to the Pegasus galaxy. However, his plans were thwarted by the actions of John Sheppard (a Detective in this reality) and Richard Woolsey. The Wraith's device is destroyed, stopping the transmission short of Pegasus, however, a rift in space-time was opened, and the transmission was sent, amplified, to other realities.

Pegasus stage
"We're gonna throw everything we have at this guy."

- Steven Caldwell

Todd urged Woolsey to attack and destroy the Hive Ship before it became a threat to Atlantis. Onboard the Daedalus, Colonel Caldwell, Colonel Sheppard and the rest of the team rushed to engage the new Hive ship. A good distance away, AR-1 proposed to Caldwell that they scout forward in a cloaked Jumper, just to make sure they were not walking into another one of Todd's deceptions. Keeping in constant contact with the Daedalus, they set off and after cloaking, Rodney McKay almost immediately began receiving readings confirming Todd's assertion that there was indeed a Hive, however, it had a significantly higher than normal energy output. McKay quickly realized the Hive was using the surplus energy from the ZPM to grow. He stated that if the Hive is able to complete its growth, the hull of the ship will be all but impenetrable. Sheppard and his team were about to send in the Daedalus when the Hive powered its weapons and fired a massive blast that just barely missed the cloaked Puddle Jumper. Sheppard realized they could be seen and decided to decloak and take evasive maneuvers so he could fire drones in retaliation. However, one of the Wraith blasts grazed the right side of the ship and Sheppard lost control. Fortunately, the Daedalus arrived and took position to cover the Jumper's escape. The Daedalus returned fire with their beam weapon, causing only minimal damage to the Hive's new, dense hull. The hive fired back, completely depleting the Daedalus' shields and causing heavy damage. Suddenly though, rather than destroy the Daedalus, the Hive jumped into hyperspace. McKay repaired the Jumper's engines and AR-1 rejoined the Daedalus. Onboard, McKay was able to decipher a Wraith transmission that was found by Kavanagh. The transmission came from another reality, and it contained the coordinates to Earth. They now know why the Hive left. McKay calculated where the Hive would have to pause between hyperspace jumps and they notified Stargate Command via Atlantis (once the communications array was repaired) and told them to send the only two available spaceships to that location.

In the Milky Way galaxy, Colonel Ellis and two of Earth's starships, the Apollo and the new Sun Tzu, failed miserably to stop the Wraith ship, with the Apollo, in bad shape herself, taking on crew from the crippled Sun Tzu. They relayed a message back to Atlantis, detailing the failure to stop the Hive and shortly thereafter, the Daedalus returned to Atlantis and was briefed on the situation. They learn that the ZPM powered Hive was the only one to receive the coordinates to Earth, thanks to its improved sensor systems. However, with the Apollo and Sun Tzu out of the way, there is nothing to stop the Hive from reaching Earth.

Meanwhile, Sheppard and McKay had the same thought: They could send Atlantis itself in defense of Earth, but it would need a full complement of ZPMs. Sheppard interrogated Todd for the location of more ZPMs, which Lorne and his team were able to locate; Atlantis now had her full complement of three ZPMs to return to Earth in a last-ditch effort to defend it. Before take-off, Sheppard was notified that he was being recalled to Earth by General Jack O'Neill to power the Ancient Control chair in Antarctica. Carson Beckett, as the second-most qualified person, took his place in Atlantis' chair and launched the city.

Milky Way stage
"It's Atlantis! They're engaging the hive!"

- Samantha Carter

Now on Earth, Sheppard was briefed on the situation by Colonel Samantha Carter and Major Paul Davis; the Hive had arrived weeks ahead of schedule and had taken orbit around the moon. For the moment, it was inactive and this was probably because it was still in the process of upgrading its systems. Sheppard proposed taking the fight to the Hive and launch a full squadron of F-302s armed with nukes. The plan went ahead, however, it took too long. The Hive was still in orbit, but had launched an inbound wave of Darts. The initial transmission that included the coordinates to Earth, also detailed Earth's defensive systems, namely the Control chair, which had been moved to Area 51. Unfortunately, in this reality, the Control chair had also been moved to Area 51, and was the Darts' target. Sheppard led the squad of 302s, outnumbered, to intercept the squad of Darts. During the battle, two Darts broke formation and headed directly at Area 51. Sheppard pursued, but his wingman was killed and his own 302 was clipped by enemy fire. As Sheppard struggled to regain control of his ship, the two Darts rammed themselves into the Nevada base, destroying the control chair. Upon learning of this, the Hive left its orbit around the moon and set a course for Earth. Sheppard pulled his ship into a steep incline; his plan was to fly the 302 in stealth mode until close enough to the Hive to blast through the Dart bay doors and detonate the nuke that had been retrofitted to his ship from inside the Hive. He was volunteering for a suicide mission.

Meanwhile, Carson had flown the city until the hyperdrive failed at the edge of the Milky Way galaxy. While Rodney attempted to fix the problem, Zelenka was tasked with recalibrating Atlantis' gate position so they could dial Earth and apprise them of the situation. As the Hive approached Earth, the SGC prepared to activate their own gate to send IOA dignitaries to the Alpha site. However, Walter Harriman notified Carter that he couldn't establish a lock, with the Alpha site or anywhere else; their Stargate was offline.

Back on Atlantis, they had established a lock with what they thought was Earth, but quickly realized they had, in fact, dialed the Hive. In standard Wraith procedure, they override the Stargate on the planet they're attacking in order to prevent their prey from dialing out. Usually this is done by dialing the planet's Stargate and maintaining an active wormhole, but in this case, the Hive had superseded Earth's gate by bringing its Pegasus galaxy gate into close proximity.

Woolsey used this opportunity to send AR-1, led by Major Lorne, through the gate to sabotage the Hive. It was at this time that Zelenka proposed activating a highly experimental and potentially dangerous drive based on the same wormhole technology as the Stargate. With it, they could potentially reach Earth in mere seconds, but if the calculations are off by even a fraction, Atlantis would be instantly vaporized.

Shortly after Lorne, McKay, Teyla and Ronon boarded the ZPM powered Hive Ship through the Stargate, Sheppard powered up his 302's engines and made his own way into the Hive via the Dart Bay. At the same moment, the rest of AR-1 was intercepted by a group of Wraith warriors and a firefight ensued. Ronon and McKay separated from Teyla and Lorne where they were taken by surprise. Ronon began fighting hand-to-hand with two warriors. Knocking one down using a Wraith spear gun, he turned his attention to the other warrior that was attempting to feed on McKay. He was able to kill it, but the previously knocked down warrior had pulled a knife and stabbed Ronon in the back. Teyla and Lorne were able to catch up to the other two and kill the remaining Wraith, however Ronon's wound was too severe and he died. More warriors appeared and Lorne forced the distressed Rodney and Teyla to leave Ronon's body behind.

Sheppard, having landed inside the Hive in the meantime, radioed the SGC and said his goodbyes. But because, unbeknownst to him, the rest of AR-1 was already on the Hive, they overheard his radio call. McKay very quickly explained the situation and convinced Sheppard not to detonate the nuke. Teyla, Lorne and McKay met up with Sheppard at the Dart Bay and McKay went to work on setting the nuke to remote detonate. At the same time, elsewhere on the ship, Kenny used his powers to restore Ronon's life. The purpose of which was to interrogate Ronon to find out how many Humans had infiltrated his ship. However, he never got the chance, as Sheppard and the rest had returned at that moment to retrieve Ronon's body. Kenny and the other nearby Wraith were easily killed. Surprised to find Ronon alive, they helped him up and quickly made their way toward the Stargate.

The Hive, now directly above Earth, powered its weapons. Carter radioed Sheppard for an update and was told by McKay that they would need ten minutes to complete their task and safely escape the ship. Samantha apologized, saying there wasn't enough time; the Hive was about to attack Earth. Sheppard took the remote detonator from McKay and once again prepared to arm the nuke while still onboard. Luckily though, Atlantis had just completed their wormhole jump and had taken position between Earth and the Hive. Carter notified the team of this fact and they continued to the Gate room.

After positioning the ship to protect Earth, Woolsey gave Beckett the order to fire on the Hive, and he did, launching several Drone weapons. The Hive returned fire. The shields held, but the sheer force of the impacts was forcing the City Ship into Earth's atmosphere. Onboard the Hive, the team had reached the gate and Rodney began work on recalibrating the DHD to dial Milky Way Stargate coordinates. The rest of the team covered him as they began taking fire from more Wraith warriors. Atlantis' shields began straining against the atmosphere and Beckett had only enough power to adjust course or to continue firing at the Hive. Woolsey gave the order to keep firing and Atlantis continued falling towards Earth.

Back on the Hive, Rodney had completed calibrating the DHD and dialed the Alpha site. Sheppard, the last one through the gate, set the remote detonator on the DHD and armed the nuke before he left. With Atlantis' shields about to collapse and the city about to be destroyed, the nuke detonated, obliterating the Hive ship.

Major Davis confirmed the kill and Colonel Carter congratulated Atlantis. But Woolsey informed them that they had lost orbit and didn't have enough power to compensate; they were going down. Uncertain if they had enough shield strength to survive reentry, they continued their descent through the atmosphere, losing contact with the SGC.

Aftermath
"So, all is well! Your homeworld was saved, you and your friends survived, and all thanks to my zero point modules."

- Todd

Everyone at Stargate Command erupted into celebration when Atlantis radioed that they had successfully reentered the atmosphere, shields intact. With little power left, the city successfully landed over water. They were able to cloak just before their approach, and the area in which they landed was placed under under naval quarantine, so for now at least, Earth's population is still in the dark.

John was discussing with Ronon, who was in the infirmary recovering from his knife wound, whether or not, now that Atlantis has returned to Earth, they'd ever let the city return to the Pegasus galaxy. Ronon was then visited by Amelia Banks, and John left the two alone. He went to see Todd, who was still locked in a holding room. Todd boasted about his help in saving Earth because of his ZPMs and asked if John had come to kill him, John did not respond. Amelia asked Ronon if he would like to take a walk, as there was something he should see. The two joined the rest of the senior Atlantis staff on a balcony overlooking the Golden Gate Bridge.