What happens with Chuck and Sarah?

According to Chuck co-creator Chris Fedak, Sarah's memory is slowly returning and Chuck and Sarah will fall in love together again; it will just take time.

From an interview with Chuck co-creator Chris Fedak:

Alan Sepinwall: I want to start at the end. They sit on the beach, Chuck tells Sarah the story of their relationship, she laughs, and we've gotten hints that she's starting to remember her life with him. And he kisses her. Does Morgan's magic trick idea work and she remembers everything instantly? Or is it just going to be a slow and steady process for her to get all her memories and feelings back?

Chris Fedak: I think I'm going to leave that up to the audience. I have my thought, and Josh has his. It's a sweet, nice moment. A happy ending for those two. I think it's up for everyone to judge that kiss at the very end.

Alan Sepinwall: Well, after last week's episode, a few commenters were upset with the idea that Sarah's memory had been erased, and that all her character growth we had spent the last five seasons was for naught. What would you say to that?

Chris Fedak: I would certainly say it's not erased. It's not all gone. It hasn't been five seasons all for naught. It's in there. And the fun will be remembering it and falling in love again. How could you imagine anything better?

Later in the interview:

Alan Sepinwall: We find out what most of the other characters are going to do, and Chuck and Sarah are on the beach, so we know they're going to get back together. But what do you see as the rest of Chuck Bartowski's life being?

Chris Fedak: Wow! Well, that's a gigantic question. I will tell you this: I see Chuck and Sarah together, being a husband and wife, starting up that computer security firm. Hopefully they won't find themselves dodging bullets for the rest of their lives. Of course, as a writer, now I start thinking, "You know what? They could get into a little bit of trouble." That gets the story side of my brain going. But for now, they're happy and they're together and thinking about their future.

In his series finale review, Alan Sepinwall gives his impression of what happens to Chuck and Sarah based on his interview with Chris Fedak:

When the amnesia storyline kicked in last week, some of you expressed concern that five seasons of character growth for Sarah were being thrown out the window. I don't think that's what happened (nor does Fedak, as you can see in our interview). Whether or not Chuck's kiss performs the Disney princess trick and breaks the evil spell all at once or not, it's clear Sarah is coming back. She remembers how to stock the Wienerlicious counter. She remembers Irene Demova. She remembers them carving their names into the frame of their dream house. And as Chuck tells her the story of their great romance, you can see her slowly beginning to connect with the rest. If she's not all the way back now, she will be eventually. He's her Chuck, she's his Sarah, and they get to fall in love all over again, and that's pretty damn sweet. We may not know exactly what the future holds for those two (Fedak also talks about that a bit), but we know that they'll be together, and all the rest is details. Once upon a time, Sarah was Chuck's guide into a strange new world, and now he gets to return the favor.

It is incongruous to imagine that they should be together at all. They were matched together by outside forces (i.e. Chuck's intersect), and she as guardian to him during his government stint. They cemented a relationship over countless missions together as a series of peril-and-save romance. Now she has lost her memory, and, conceivably, her skills. They have no need to save each others' lives any longer, so this is no longer a workable scenario.

Absent this, he stands as much a chance as the next "6" guy to get with a "10". Perhaps FOX can revive Beauty and the Geek for them

BennyMcBenBen's answer is probably as authoritative as you will get, unless they create a spin off or resurrect the show. But I can answer from other "similar" real life examples.

I saw the movie "The Vow" recently. It was based on a real life event (which was chronicled in a book) where a man's wife lost her entire memory of him. Last thing she remembers is being engaged to another man. Her husband reacted a lot the same way as Chuck - trying to get her to fall in love with him again (except without all the spy stuff).

This movie was also similar that the person she remembered being would never be interested in her current husband. She had forgotten a lot of personal growth and changes she went through that made her the person who fell in love with her husband. Her former fiancee was very successful (much more so than her current husband) and wanted to get back together with her (she dumped him originally).

At the end of the movie we are told that the real life couple it was based on got back together, but she never regained any of her memory.

So in "real life" it has worked out in similar circumstances.

I completely agree with the director's statement. Sarah maybe forgot her life with Chuck, but we can see that she is remembering slowly (Irene Demova,their dream house). Finally, she said to him "kiss me", so clearly, she wants to be with him, but,they will have to fall in love again. They will be together, but it would take time.

Chuck spent 5 years with Sarah and raising him self up from a nerdy loser to the CIA's top spy. He is now currently on the same professional level, personal level (dresses with class,had a better hair cut, much more confidence ect.), and Sarah and has spent 5 years getting to know the real her and not the tuff exterior she had in episode 1. So realistically chuck knows the real Sarah better than anyone else and is perfectly "in her league" as of this point in terms of confidence, style, looks and physical spy ability. To Sarah chuck would be irresistible relationship partner because the personal connection they'd have established seemingly instantly to Sarah could not be matched by any other guy especially with the added help of memories returning little by little. Therefore chuck is Sarah's perfect guy.

To be honest, it can end every way you can imagine. Sarah forgot the last 5 years, but she didn't forgot her skill cause she learned them before.

Yes she is WAAAAAAAY over Chuck's league and yes they fell in love just cause they were working together and she had time to know him. In real life there are slim to non chances to get woman like that in just one attempt. And that is all you'll get.

The show ended with Chuck's attempt to get her back and Sarah watching her personal video diary thus her willing to give him another chance. From that point you can think whatever you want: either Chuck did win her back or he failed.