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 Ronan, 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.

McKay and Ronan, each unaware of the other's motive, volunteer to assist Dr. Jennifer Keller with a medical follow-up away from Atlantis. But once in the settlement, a nervous child patient prompts Keller to ask Ronan and McKay to wait for her in the local tavern while she finishes her treatment. Later, when the pair return, they are surprised to learn that she left sometime ago. An exhaustive search of the village turns up no sign of her. But a set of footprints in the dirt just past the village confirms Ronan's mounting suspicion that Keller has been kidnapped. Ronan, wasting no time, begins to track her abductor while McKay runs back to the stargate to radio for assistance. But just as he reaches the DHD, four Hunter Wraith come through the gate and fan out in separate directions. Ronan, knowing full well that these Wraith exist to chase Runners, suspects there is a connection to Dr. Keller's disappearance. And he knows he must draw on his uncommon skills as a former Runner if he is to save her.

Keller and the Atlantis team meet with the wraith, Todd, to deliver a startling proposition. Aided by her studies of Michael's retrieved data, Keller believes she has found the means by which to "cure" the Wraith of their need to feed on humans. All she requires are some wraith willing to act as test subjects for this breakthrough treatment. Todd is intrigued, but insists that they must first win the support of the Primary - the supreme Wraith Queen in the alliance. But to do so, Teyla must go undercover with nothing to rely on but her wraith DNA and an ally with a hidden agenda.

Dr. Beckett is asked to delay his departure from Atlantis when word comes that Major Anne Teldy and her away team, Sgt. Dusty Mehra, Cpt. Alicia Vega and Dr. Alison Porter, have stumbled onto one of Michael's labs inside an extensive underground catacomb. He and Lt. Col. Sheppard gate to Teldy's location, where further investigation reveals an abandoned laboratory containing numerous stasis pods. While Dr. Beckett and Dr. Porter stay behind to sift through the research data that Michael left behind, Sheppard and Teldy's team set out to explore a nearby village. Beckett and Porter conclude that Michael was experimenting on the genetic characteristics of several different life forms. Meanwhile, Sheppard and his team arrive at the village to find it abandoned. Yet chilling walls of fog and flashes of movement within it suggest that they are not alone.

En route to check on a missing research team, Lt. Col. Sheppard, Dr. McKay, Teyla and Ronan emerge from the stargate to find themselves swimming atop a flooded valley. With only the apex of the gate accessible above the waterline they cling to it - soaked and bitterly cold - until a puddle jumper can make it through to rescue them. But during the flight back to Atlantis, McKay inexplicably falls ill and in the days that follow, his condition declines further. Dr. Keller discovers a parasitic organism in his brain that cannot be surgically removed. As a result, his ability to function continues to deteriorate to the point where he has virtually no recollection of who he is or what he is capable of. Soon, his emotions and memories have regressed to those of a young boy and, fearing that he will not pull through, the doctor summons Jeannie, McKay's sister, to say her final goodbyes. But it's too late. Rodney no longer recognizes her or any of his friends. However, Ronan has a plan, albeit a very risky one.

David Hewlett (Dr. Rodney McKay) answers fan questions from the Forum in this special Q&A series.

Joe Flanigan (Lt. Col. John Sheppard) answers fan questions from the Forum in this special Q&A series.

Amanda Tapping (Col. Samantha Carter) answers fan questions from the Forum in this special Q&A series.

Jewel Staite (Dr. Jennifer Keller) answers fan questions from the Forum in this special Q&A series.

Amanda Tapping (Col. Samantha Carter) answers fan questions from the Forum in this special Q&A series.