Ghost In the Machine

S5 E5: Returning from an exploratory mission the team is mystified when an arc of blue energy causes the puddle jumper's primary systems to shut down slamming them into an active stargate. They narrowly make it home only to be greeted by similar erratic anomalies within the city itself. Soon nearly every system in Atlantis is affected by ominous power disruptions. Suddenly a puzzling message appears on McKay's computer screen. Its author claims to be a former friend long thought dead. Now an incorporeal presence she begs Rodney to utilize the Ancient's technology to build her a new body. Highly skeptical the Atlantis team is faced with an impossible decision. To create the means to release an entity who may or may not be a friend or stand by as it systematically destroys the city's technological infrastructure.