The CIA, led by Decker, issued a kill order for Morgan because he was telling everyone that he was the Intersect, and the team asks General Beckman for help. Finally, in "Chuck Versus the Business Trip" Morgan gets the Intersect removed with the help of General Beckman.

Does Chuck get the Intersect back in Season 5?

The season five arc with Morgan having the intersect turned out okay. ... Yes Chuck (Zachary Levi) gets the intersect back in the final episode but that was too little too late. The second is the relationship between geek/ nerd turned hero, and the girl he could never get.

What happens to Morgan in Chuck?

In the Season Five episode, Chuck Versus the Frosted Tips, he dumped Alex via text because of the corrupted Intersect. He apologized to her later but she said that they cannot be together again but they can still be friends. In the end they reconcile and eventually move in together.