Col. Abraham Ellis, commander of the new Earth ship Apollo, barrels into Atlantis on a single-minded mission. Intel indicates that the Asuran Replicators have been building an armada of ships to attack Earth, so Ellis's orders are to launch a massive pre-emptive nuclear strike against them. Disregarding Dr. Weir's serious doubts, Ellis attacks Asuras, leaving the Replicators' homeworld a smoking ruin.
But Weir was right to be concerned. The Replicators haven't been destroyed, only provoked. They retaliate against Atlantis with an insidious weapon: a stargate mounted on an automated craft that flies it into orbit over the city. Once in position, the stargate activates, and the Asurans send through a devastating energy beam. Not only will the beam soon rip apart Atlantis's shield, but also, because the orbital stargate is in continual operation, Atlantis's own 'gate is useless. The team is trapped.
After Ellis fails to destroy the orbital stargate with the Apollo, Weir reasserts her own authority. The Replicators dismiss her attempt to negotiate, so she permits McKay to sink the shielded city to the ocean floor. The water attenuates the Asuran beam and buys the team a few more hours - nothing more.
It's just enough time for McKay and Sheppard to conceive a radical plan. If they can corral enough power, then they can activate city's stardrive and fly to safety. Quickly, McKay augments Atlantis's Z.P.M. with power from the underwater Ancient drilling station. Then Maj. Lorne and a team of F-302 pilots redirect an asteroid's course so it will interrupt the Asuran beam just as the city takes off, allowing McKay to transfer power from the shields to the stardrive for a few crucial seconds. Finally, Sheppard sits down in the Ancient control chair and orders the city to take flight.
As Atlantis lifts off, the Asuran beam breaches the asteroid, lances down, and grazes the city's control tower before McKay can re-establish the shield. Everyone in the tower is wounded, and Weir, especially, is seriously injured.
Sheppard accelerates the ship into hyperspace and hurries to help his friends. They've barely begun caring for the wounded, however, when the ship drops back to sublight speed. McKay can't figure out why, which means they're stranded in the middle of nowhere with only enough power left to keep the shield up for a day. If the shield collapses, they'll all be exposed to the deadly vacuum of space, and their great escape will have been for nothing...