We pick up with Chuck and Sarah trying to rescue Orion from Fulcrum. Things heat up between the two when they realize that their feelings for one another are more than just a cover.
Casey is given a promotion and ordered to recover the rogue team, dead or alive.
Just as Chuck and Sarah get close to finding Orion, Casey captures them. They eventually escape and now have to rescue Awesome who was trapped in Casey's apartment, while trying to find clues about where Chuck might be. In the process, Chuck's secret comes out, and now Awesome has to help cover for Chuck with Ellie.
When orders come down that an air strike has been ordered where Orion is being held, Casey joins up with Chuck and Sarah in a daring rescue to save Orion and take down FULCRUM. Meanwhile, Orion finishes the new Intersect, and Ted Roark attempts to build an army with it.
While Sarah and Casey infiltrate the FULCRUM base, Chuck discovers Roark's plan and tries to stop him. Casey, Sarah and Orion return to find Chuck captured and are subsequently captured themselves. Roark projects the Intersect hoping to make his army. Orion has instead programmed it to remove the Intersect from Chuck. Just as Roark realizes what has happened and orders Chuck and his team to be killed, the air strike begins. This gives the team the perfect opportunity to steal the new Intersect device and escape.
Finally, Chuck gets to relax and go back to his normal life; or does he? The episode ends with Roark emerging from the strike zone and saying that he is heading to a wedding.