Colonel Sheppard's team finds a world where the leader lives in a tower that possesses the power to stop Wraith attacks.

The team investigate rumours of an invincible hero off-world, only to find Lucius Lavin again manipulating a hapless village.

Rodney McKay awakens in his lab, tied to a chair and with no memory of who or where he is. He did seemingly leave himself a video message telling him to look for Teyla. The problem began some 14 hours before when Dr. Katie Brown returned to Atlantis with plants from a planet she had visited. The plants had been cleared through the normal quarantine procedure but she is soon afflicted with severe headaches and loss of memory, eventually falling into a coma. Memory loss begins to afflict other members of the crew but they soon become distrustful of one another, making conclusions based on false assumptions and a misreading of the situation. Fortunately, there are two members of the team who seem to be immune.

When McKay's sister Jeanie is kidnapped, the team returns to Earth to find her.

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.

The new race that stole the device, not to mention Rodney and Daniel, turns out to be an old one meaning very old and well known to the human race. With an ancient grudge to settle, they force Rodney to activate the device against the Wraith with a side effect that could kill millions throughout the galaxy. That makes the Wraith mad so they abscond with the Daedalus to retaliate. Once again we lowly humans have to take control of a messy situation to keep the master races from wreaking havoc in the galaxy.