Plot summary
Daniel Jackson returns to Atlantis to do research on the Lantean scientist Janus. But after finding one of Janus' secret labs, McKay and Dr. Jackson disappear after an alien ship appears in Atlantis and First Contact goes less than well. Woolsey boards the Daedalus with Ronon and Keller to meet with Todd to discuss Dr. Keller's gene therapy. The aliens force McKay and Jackson to activate a device that will destroy Wraith ships when they enter hyperspace, but with the side-effect that Stargates will explode when they are activated. Todd believes he has been betrayed and hijacks the Daedalus while Atlantis manages to track down McKay and Jackson but has the Stargate explode when trying to reach the Daedalus to reach the planet as it has no Stargate.
Credits
Adapted from Wikipedia contributors, Stargate Atlantis season 5. HTML formatting and reference markers removed.