The Daedalus arrives and the two hive ships are destroyed. Atlantis seems saved, then Zelenka detects 12 more ships. Ford seems changed after a fall in the water.

McKay, Sheppard, Beckett and Weir are on the Daedalus. McKay finds a Wraith virus that is infecting ship systems and sending a signal to the Wraith.

The Trust, a Goa'uld terrorist organization, has planted a bomb in Atlantis.

Atlantis helps with repairing an Ancient shield generator on Taranis. They discover the Taranians are in possession of an Ancient warship.

The hive ship approaching Atlantis is Michael's. He wants a trade: the retrovirus for not revealing the secret of Atlantis and insights on Wraith technology.

Fallen into the Wraith trap, McKay initially resigns to fatal captivity in a cocoon, but Ronon keeps struggling to attempt escaping, or at least taking some Wraith down with them. Sheppard managed to hide his glider on the very hive ship, seeking a way out, surprised to get radio contact with Michael, who seeks revenge after the ingrate queen has him semi-restrained as 'too human' suspect. While they try to sabotage the hive and maybe escape, the Daedalus and Orion race just in time to fight the two hive ships before they may attack earth. Weir is summoned to SGC for a pointless grilling by the International Oversight Advisory, finding them bureaucrats unable to risk a decision beyond questioning what was already done. So she returns, never mind the career risk compared to a Wraith culling. Sheppard manages to reach the Daedalus and his party comes up with a daring plan to overpower the hive with the weaponized retrovirus, despite bombarded damage compromising even their life-support systems.

Rodney's sister is brought to Atlantis to make use of one of her theories.