The episode opens with Sarah and Chuck waking up together and Chuck tells Ellie and Awesome that Sarah and he are getting a place together. Meanwhile, poor Cole is getting tortured and shows up saying he escape dand didn't say a word about the Intersect. Casey and Sarah get sent to investigate a scientist known as Perseus at a consulate ball. While they're there, Chuck and Cole are in the van doing surveillance. Chuck flashes on a scientist they realize must be Perseus and when Sarah approaches him, whose real name is Howard Busgang, she and Casey end up getting caught.
Cole and Chuck attempt to go in to rescue them and Cole even gives Chuck a gun to go in. Chuck ends up getting caught in a window and accidentally shooting Busgang in the leg but distracted the bad guys long enough for Casey and Sarah to break free. However, on her way after the Fulcrum agent that tortured Cole in the beginning of the episode, Sarah gets shot at and Cole jumps in the way of the bullet. Although Chuck is humiliated when he complains about his sprained ankle compared to Cole's bullet wound, he heads to the hospital where he runs into Busgang being treated for his gunshot wound.
Chuck follows Busgang back to his lab where Fulcrum agents follow them. Chuck discovers that Busgang worked on the Intersect and flashes on a folder marked Orion. Busgang explains that Orion invented the Intersect and might know how to remove it and just as he says more, the Fulcrum agent enters and shoots him. Just as he's about to get Chuck, Cole dives in and saves him. However, just as the guy goes to shoot Cole, Chuck tries to save the day by going for the agent's legs and successfuly knocks him down. However, Chuck forgets to grab the gun and soon both of them are held up at gunpoint until Sarah comes in to save them both.
At the end of the episode, Cole's work is done and he's set to leave, but asks Sarah to come with him on his jet. She says no and says she doesn't cheat on her cover boyfriend because when you meet someone you care about it's tough to walk away. Chuck then tells Sarah he can't live with her because he's crazy about her and living with her would be too much. He does tell her though his new goal is to get the Intersect out of his head so he can live happily ever after with her. He then goes to his Tron post and writer Orion on the back of it.
Meanwhile, throughout the episode Morgan was dealing with Anna's mistakenginly seeing his lease papers that were meant for him and Chuck. Anna thinks it's a gift for their 16 month anniversary for them to move in together. Morgan, with the help of Jeff and Lester, attempts to scare her out of living with him. Soon he realizes thanks to how understanding she is and advice from Chuck that he doesn't want to scare her off. Before Chuck can even tell Morgan he can't live with him because he's going to live with Sarah, Morgan tells Chuck he's going to live with Anna.