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 Dr. 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 Ronon, have joined Colonel 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 them of betrayal, takes control of the Daedalus.