Why is the Intersect removed from Chuck at the end of 4.07 First Fight? What is the purpose of leaving Chuck without the Intersect from 4.08 Fear of Death to 4.10 Leftovers? Upon first watching the show, some viewers thought it was a test by the CIA to see whether Chuck can be a spy without the Intersect.
I think it is absolutely a test, but not in the sense that it is a government test to see whether Chuck can be trained as a real spy without the Intersect. It’s a test by the writers to see whether Chuck and Sarah’s relationship is based on the Intersect and will crumble without it.
This show is a constant exploration of a complicated and most unlikely relationship between a spy like Sydney Bristow (Alias) and a nerd like Jim Halpert (The Office). It explores obstacle after obstacle to this relationship and makes Chuck and Sarah overcome the obstacles to prove the point that they are perfect for each other.
In this arc, Chuck is stripped of the Intersect to see whether he’s worthy of a super spy like Sarah without it. This is put in Rye’s words, “Are you a spy? Or are you a guy with a spy girlfriend?” And we can see Chuck’s insecurities surface, and also Sarah’s own doubts and fears when she unwittingly humiliates him before Casey, Rye, and Beckman when Chuck says, “I’m a spy,” and she yells, “No, Chuck, you are not!”
And so Chuck is put in yet another catch-22 situation (after the one in his red test episode)—now he thinks he needs the Intersect to be worthy of Sarah, but Rye tells him that he must forget his love for Sarah to get the Intersect back. And Chuck chooses his love for Sarah over the Intersect.
And in the next episode, Sarah will move heaven and earth to prove to Chuck (and us viewers) that her love for him is not based on the Intersect but on him. Once that point in very clearly made in Phase Three, Chuck can get the Intersect back.
But, of course, the writers are not going to let this question “is Chuck a real spy without the Intersect?” go unexplored.
And that’s where season 5 comes in. The whole season is there to make the point that Chuck has indeed become a real spy even without the Intersect, and the master episode that clearly makes this point is 5.07 Santa Suit, which is the reversal of 4.09 Phase Three. In this episode, Shaw renders Sarah powerless, just as the Belgian did with Chuck in Phase Three, and Shaw taunts Chuck that Sarah is the superior spy, and Chuck will move heaven and earth to save Sarah against an Intersected Shaw who has all the advantages.
You can rest assured that, after 5.07 Santa Suit, Sarah, who still had doubts at the beginning of the season, will never again say that Chuck is not a spy without the Intersect.