As the Hive ship arrives above Atlantis, everyone is happy to find that Col. Sheppard and team are in control. However, the Wraith crew, now turned back in to humans using Dr. Becket’s gas, must be dealt with in some way.

Michael, who now has separately been reverted back to his human form, and the reverted Wraith crew, are relocated to an unpopulated planet which lacks even a stargate. Dr. Beckett then refuses to leave the planet until he is sure the former Wraith won’t revert back to their former state, as Col. Sheppard and team plan to leave back for Atlantis.

At the same time, IOA Agent Richard Woolsey travels back to Atlantis with Dr. Weir to evaluate her command there.

Things do not go as planned, and Dr. Beckett's life becomes endangered. Sheppard and his team must take the crippled Hive ship back to try to rescue him, as a second Wraith ship approaches the planet Dr. Beckett was left on.