- Dr. Daniel Jackson comes to Atlantis in search of a lost Atlantian room. The discovery reveals a new race. Daniel and McKay are kidnapped by the new race and are forced to finish a device which may kill the Wraith. Todd feels betrayed and takes the Daedalus.—Anonymous
- Rodney McKay and a visiting Daniel Jackson find a long lost room in Atlantis that served as a laboratory for the Ancients. Their entry into the room triggers a signal however and the city is soon invaded by an unknown race who steal a device from the lab and kidnap McKay and Jackson. The device is a powerful weapon that will destroy any Wraith ship jumping into hyper-space. Meanwhile, Dr. Keller's gene therapy to allow the Wraith to survive without having to feed on humans is ready for testing. Todd the Wraith has arranged for them to serve as guinea pigs but when two of his ships are destroyed while jumping into hyper-space, he assumes the Earthlings are responsible and takes over the Daedalus.—garykmcd
- Stargate SG-1's Dr. Daniel Jackson travels to Atlantis when his research suggests that a rebellious Ancient scientist named Janus may have hidden a secret lab somewhere within the city. Hoping to find it, and possibly a significant portion of his unauthorized research, Jackson enlists McKay's help.
An obscure log entry leads them to a cloaked lab where they unwittingly activate a signal on a distant planet. Hours later, the city is paid a visit by a group of mysterious aliens.
Meanwhile Woolsey, along with Dr. Keller and Ronan, have joined Col. Caldwell on board the Daedalus, leaving Sheppard in charge of Atlantis. They welcome Todd and his delegation to the ship to discuss testing Keller's gene therapy on live Wraith subjects. But events take a turn for the worse when Todd, suspecting betrayal, takes control of the Daedalus.
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