While watching this episode I realized what had been missing all season long. A believable motive for the "Dark Side Intersect". Let's be honest, casting Brandon Routh was a mistake. He's not believable as a super spy, neither ruthless or charismatic enough. He's got zero on screen chemistry and he seems two dimensional in comparison with just about everybody else in the cast.
Had I been the show runner, I would have done things differently. The character of Shaw should have been a woman. Someone that exudes charsima, experience, decisiveness, ruthless manipulation. I would have cast someone like Heather Locklear as an older, better, more experienced Sarah Walker to run the team and move Chuck off the dime as the intersect. Someone that Chuck idolizes, is intimidated by, is attracted to, fears, loves. She would have ordered Sarah to revive the cover relationship with Chuck but Shaw would have been Chuck's personal trainer. Then I would have an multi-episode arc where Sarah is positioning herself to leave as part of an overall plan where Shaw (because of similar features) would replace Sarah as Chuck's cover girl friend. But, here's the twist, Beckman contacts Walker and Casey off the grid (more on that in a second) and reveals that Shaw is a Ring agent, a master manipulator and is trying to false flag Chuck to work for the Ring. Beckman orders Walker and Casey to get evidence that Shaw is Ring to prove to Chuck that she's Ring and prevent Chuck from turning dark. But, the kicker is, they must let the training go on as much as possible to get Chuck fully operational and to not let him know what's going on. Sarah has to continually try and convey subtle things that all is not as it appears and that she still loves Chuck, while keeping it all from Shaw and appearing to go along with the overall plan.
I'd have done an episode, where instead of set piece actions and explosions, we see Casey and Walker, separately use old school trade craft to really disguise themselves to meet with Beckman. And no, not some cheesy glasses. Instead of spending tens of thousands of dollars on explosions, spend a couple of thousand on wigs, masks, prosthetics so they really don't look like themselves. Then build up the suspense as they try to figure out who Beckman is, when she's also in disguise. And a shocking reveal when they find out Beckman is the one fingering Shaw and the reasons.
Final episode. The climax is a scene where Sarah and Shaw battle for Chuck's very soul as he's torn between the woman he loved (Sarah) and the woman he worships (Shaw).
Just my ..02