The rescue mission to Atlantis starts with a bang. With McKay, Ronon, Teyla, Weir and Beckett aboard, Sheppard flies a Puddle Jumper through the stargate straight into Atlantis's gate room. There, McKay drops an explosives package as the ship takes heavy fire from the humanoid Asuran replicators now holding the city. Sheppard also makes radio contact with Gen. O'Neill and Richard Woolsey, who are hiding in the bowels of Atlantis. Then Sheppard punches the ship through a wall to safety just before the explosives wipe out most of the city's stargate operations center.
Sheppard flies his team into orbit. They have only a short time to complete their rogue mission before the Daedalus arrives from Earth with official orders to bomb Atlantis into oblivion. After retrieving their old nemesis Niam from where he floats in space, Sheppard's team flies back toward the city, planning to use the dormant Asuran to plant a virus in his fellow replicators. Unfortunately, the replicators attack the team's Jumper with drone weapons, driving it to the dubious safety of an underwater Jumper bay.
This water-filled chamber turns into a trap, threatening to drown the leaking Jumper until O'Neill boldly swims to the manual controls and frees the team. The maneuver exposes O'Neill and Woolsey to the replicators, who seize them and probe their minds. Learning the humans' plan from these probes, the replicators awaken Niam themselves. Niam attacks, forcing McKay to disintegrate him with an anti-replicator weapon. The first rescue plan has failed.
After some urgent brainstorming, the team splits into pairs. Sheppard and McKay hurry to O'Neill and Woolsey's holding cell, where McKay tells the prisoners that the team is going to plant C-4 explosive on all the city's shield emitters, which will destroy the city's shield and ensure that the Daedalus's attack will succeed. Before McKay can free O'Neill and Woolsey, however, replicators close in on the cell. McKay and Sheppard flee, leaving behind two prisoners who now know the second top-secret plan of the day. If the replicators probe O'Neill and Woolsey's minds again, they'll know all about the C-4.
Nonetheless, the pairs of humans sneak through the city, sabotaging the shield emitters. They succeed - barely - but are then immediately captured. Inevitably, their enemies have discovered their plan by probing Woolsey's mind. The replicators now have good reason to believe that victory is theirs at last.