While trying to retrieve a bomb, Sydney and Vaughn are ambushed by unidentified assailants. Meanwhile, Lauren and Sark continue to solidify their new partnership, Sloane divulges a dark secret to Dr. Barnett and Marshall shows the strains of new fatherhood.
Additionally, a seven-minute animated short entitled Animated Alias: Tribunal was produced for the DVD release of the third season.
Vaughn helps Sydney escape before being arrested by the National Security Council and Lauren tells Dixon that he is no longer in charge of the task force due to his hiding of evidence concerning Lazarey's murder.
It was Sydney who had performed the murder, during a test of loyalty (explained in Episode 11).