Atlantis is out of options: The remaining two Wraith hive ships are only hours away. The Atlantis team has no choice but to evacuate. Weir orders the self-destruct set, the virus that will destroy the Ancient database downloaded and the Alpha site dialed.
Incoming wormhole: The IDC is from Stargate Command. Col. Dillon Everett and a platoon of Marines arrive with a massive arsenal of small arms. Everett salutes Dr. Weir and conveys Gen. Jack O'Neill's compliments on a job well done under extraordinary circumstances. He then relieves her of command by presenting signed authorization from O'Neill himself. Everett's first order: Cancel the self-destruct. He and his troops are here to defend Atlantis at all costs.
Everett is up to speed on Atlantis' situation, having gone over every scrap of information in the compressed data message the team sent weeks earlier. He explains how a ZPM was found in Egypt during an archeological dig. It was used to power his team's journey through the stargate to the Pegasus galaxy. The ZPM is, at this very moment, being transported up to the battlecruiser Daedalus, which is the Prometheus' sister-ship. The Daedalus will arrive at Atlantis with the ZPM in less than four days. That is how long they have to hold this base against the Wraith. The ZPM will then be used to power up Atlantis' force field. Everett orders Maj. Sheppard to dial up the Alpha site and recall all military personnel as well as any civilians who would like to return and take part in damage control.
Uncomfortable with Dr. Weir out of the tactical loop, Sheppard warns Everett that if he alienates her, he will lose the respect and support of everyone on Atlantis - including Sheppard himself. Everett allows Weir to sit in on the tactical briefing.
The plan is to place six Naquadah-enhanced nuclear warheads as space mines between the Wraith armada and Atlantis, using the jumpers. Everett's pilots are being injected with an Ancient gene-therapy regimen and will be trained by Maj. Sheppard on jumper flight ops. Massive rail guns are emplaced to defend the city. Everett has also brought a Mark-II Naquadah generator that will power Atlantis' chair weapon.
Dr. McKay gets the chair weapon operational, but there's a problem: There are only a few dozen drone weapons left in the chair. The thousands it's supposed to contain obviously were used during the Ancients' last fight against the Wraith.
The alarm sounds. A hundred-plus asteroids are heading toward Atlantis. The Wraith have harvested them from the system's asteroid belt and accelerated them from a safe distance, for the express purpose of setting off the mines - which they do, taking out Atlantis' first line of defense.
With the city's sensors blinded by the Naquadah-nukes, Wraith darts approach the city undetected. They expertly evade the rail guns' barrage and fire on the city. Some darts make kamikaze runs. The gunners at the control tower are culled up to the Wraith ships. Sheppard mans the chair weapon and destroys several Wraith darts with the powerful drones. The wave of Wraith darts is neutralized.
Unfortunately, the chair weapon is out of drones, and the deep-space sensors are still blind. Everett is open to suggestions. Sheppard has a plan: If McKay and Dr. Zelenka can find a way to remote-control a jumper, they can fly it right down the hive ships' proverbial throats. Unfortunately, all the nukes were destroyed by the asteroids....
Weir bargains with the Genii on their homeworld. She'll give them the C-4 explosives they've so desperately wanted in exchange for their prototype nuclear bombs, which will be tested on Wraith hive ships at no risk to the Genii. They accept the bargain.
Meanwhile, Teyla has felt the presence of the Wraith. They are in the city. Everett arms Teyla and other Athosians. They, Sheppard, Lt. Ford and the other soldiers hunt them down and kill them. Some Athosians are killed in the process.
Weir returns with the nukes. McKay and Zelenka get them operational and also succeed in getting the chair weapon to remote-pilot a jumper. The nukes are loaded aboard the jumpers. The hive ships are in range. Wraith darts are heading toward the city. The rail guns destroy one.
More Wraith are in the city. Everett comes face to face with one, but Teyla cannot be raised by radio. Ford and his soldiers are trapped in a standoff with a Wraith patrol.
Then, another setback: The Mach II Naquadah generator powering the chair weapon is depleted. There is no way to remote-pilot the jumpers.
With no other choice, Sheppard gets into one of the nuclear-armed jumpers and pilots it straight toward the armada.