On Earth, a galaxy away from Atlantis, Gen. Landry receives intelligence that The Trust, a group of conspirators controlled by the evil Goa'uld, have learned of the Ancient city and sent an undercover operative there to plant a bomb. Details are sketchy, but any use of Atlantis's stargate to dial Earth will somehow trigger the explosion.
The moment that Earth relays this news to Atlantis, Dr. Weir orders both the stargate and the city's main power source, a ZPM, shut down. She also orders the absent starship Daedalus to return, because the bomber might be trying to escape aboard it.
In the midst of this intense search for both bomb and bomber, the city's distress beacon activates. Before McKay can shut it off, it catches the attention of two Wraith cruisers, who head straight for Atlantis. If they discover that the city still exists, they will attack immediately. To prevent such a catastrophe, McKay prepares to reconnect the ZPM and use its power to cloak the city from view.
Meanwhile, Teyla finds herself occupied with a very different concern. Charin, her beloved adopted grandmother, is seriously ill. Although Charin urges Teyla to accept her death as inevitable, Teyla begs Dr. Beckett to heal her friend. When he explains that he can save Charin's life by installing a pacemaker for her heart, Teyla is elated, but the old woman reiterates her desire to die a natural death and gently orders Teyla to respect her wishes.
With the exception of this private grief, suspicion is consuming the city. McKay suspects that Lt. Cadman, a demolitions expert, is the saboteur. Weir suspects Dr. Kavanagh, a disgruntled scientist. For his part, Kavanagh suspects Dr. Zelenka, who is off-world on a conveniently timed mission. Weir's suspicions carry the most weight, however, so the investigation's focus settles on the prickly and defensive Kavanagh.
Then McKay discovers that no actual bomb exists. Instead, the saboteur has removed the failsafes from the ZPM, so that it will overload in a massive explosion as soon as it emits any significant amount of power. The saboteur has been trying to provoke them into dialing Earth or cloaking the city - either of which will cause an overload.
But the Wraith are closing in. In desperation, McKay shuts down as many secondary systems as possible and activates the cloak. As the power usage levels inch toward critical, Weir considers torturing Kavanagh for answers, and Charin hovers near death. Atlantis teeters on the brink of destruction, though whether it will come from without or from within remains to be seen.