
Spoilers: Chuck vs the Ring
Ship Chuck/Sarah
After rewatching a clip that included the final finale scene from the time Chuck drops in , I had a very evil thought. What if Bryce is brought back again but this time working for the Ring (whether willingly(eventually) or unwillingly you choose) plus he has all the info and encoding from the new Intersect in his head because when he died he died with his eyes open. If he wasn't brain dead completely he could probably receive the info.
The payoff - a Chuck vs Bryce Battle Royale with Bryce leading on the experience knowing how to fight but Chuck having caught up for the most part by finally being trained not to mention that Chuck seems a better planner than Bryce.
Even if you have Bryce be a good guy you acan have the battle happen because Chuck finally let's loose all his frustration at the harm Bryce has done to him in the name of protecting him and how Bryce basically co opted everyone Chuck loves (his father, Sarah, Jill) at least temporarily and how he's never apologized and doesn't seem to get that he had no right to make decisions like that for Chuck.

Spoilers : possibly up to Lethal WEapon
Ships: Chuck/Sarah, Bryce/Chuck
For this both Bryce and Chuck would have to be bisexual even if neither one of them acted on it. Chuck may have realized he had feelings for Bryce as well as Jill in college but by that time , he was dating JIll and he wasn't a cheat. He then buried any sexual feelings towards men deep because he associated them with Bryce and his betrayal.
Basically this is to be Bryce and Sarah warring to win Chuck's heart. The timing would mean that Chuck had recently seen Sarah dancing attendance on another man (not to mention the trauma of having to listen to her in the hotel room through the earpiece) . NOt to mention he then chose to move in with Morgan and when given the chance to move in with her told her no.
I like unrequited love as a reason for Bryce's actions both in college and in sending him the Intersect because it falls less under egotistical screwup and is more in line with love makes you crazy, unrequited love doubly so. Plus wierdly enough it makes Orion trusting Bryce ok if he knew Bryce was in love with Chuck not to mention it makes all those times he got in between Chuck and Sarah come out as him trying to keep Sarah away from Chuck not the other way around.
It's up to the author whether or not he ends up with Bryce, Sarah or is in a time-share relationship where he splits his time with them .
It's also up to the author whether or not Chuck has sex with one or both.I prefer both at different times because he wouldn't really be in a relationship with either one until it was stated out right and therefore no cheating happened. Maybe have Chuck have sex with Bryce and then wake up freaked out because he had sex with the man who he hated for so long and did so much damage. Could have him sneak off while Bryce pretends to be asleep and is hurt.
Maybe have Bryce show up after having to spend some time off his feet (in a hospital or with a broken leg) and have him start to review his life and realize he didn't have the right to make that choice for Chuck.
This came about from reading a bunch of slash fic and a bizarre desire to redeem Bryce. I think he still had a lot to answer for and they shouldn't have killed him.
I got a what if or two for season 3 = possible fanfic prompt.
Going on the assumption that the Intersect abilities can spontaneously activate (the way he spontaneously flashes) even though he now knows he can trigger flashes. What if the Intersect triggered in Chuck's sleep? To do anything at all. And as a separate prompt or together with the first one-What if one of the abilities in the Intersect is sexual (gay and straight) ?
It could be horrifying if it had him act like that towards someone he had no interest in (Like a man because he reads as straight or someone like Carina who he's turned down because he's in love with Sarah) or if the Intersect tried to initiate sex with Sarah (while she was sleeping beside him for the cover only because she's running scared again) while he was alseep. Would she recognize what was happening and wake him up to stop it or would she not realize and sleep with him without him being aware and just thinking it was a dream when he woke up.

Spoilers Chuck vs the Alma Mater
Ship Chuck /Sarah or gen.
Differences: Bryce is known to be alive and that he wasn't really with Fulcrum. Chuck doesn't flash on himself and flat out refuses to go to Stanford. He's left behind either with a bodyguard (maybe Carina) or he's in the Castle on lockdown.
Bare bones. Bryce has heard about the Professor being in danger and shows up. He asks after Chuck and is told about Chuck's refusal .When he asks why Chuck refused Sarah goes off on him . He tries to explain his reasoning to them but it's pointed out that surely there was another way and he could have told Chuck what was going on even though he wasn't supposed to tell that he was CIA (but since interfering in the recruiting process was probabaly a no no that his boss would frown upon, he could have made an exception). Sarah points out how devastated Chuck was and how he seems to not really trust anybody but Ellie and Morgan (trusting Sarah and Casey is strictly because he had too) .Maybe include something about how he couldn't continue his academic career on account of being thought a cheat.
Basically I want Bryce to get how much damage he did and how something that major wasn't his decision to make.
People have compared what Bryce did to Chuck going off on Morgan to protect him in Best Friend but there were differences. Morgan was in immediate danger not to mention Chuck tried to make things up to Morgan as soon as possible. Also Chuck realizes how much Morgan was hurt by what he said. Bryce doesn't seem to get that he inflicted damage, nor did he try to make things up to him.
POssibly have Bryce tell them about being in contact with Papa B.
ship: Chuck/Sarah (main) also Awesome/Ellie, Anna/Morgan and any other existing ships.
Spoilers through vs The Ring.
One minor change to Jeffster's act. No roman candles to set off the sprinklers. Also Ellie isn't blocked by Chuck and Sarah looking like they just had a quickie (her dress being torn , him tucking in his shirt) and manages to get to reception area to see broken skylights, Special forces, people on the ground, her father and a supposed to be dead Bryce Larkin among the debris.
Possibly have a freaked out Ellie scream at the top of her lungs and attract the attention of the guests because Jeffster's act is over and no longer drowning out anything else .Which would mean there's a lot more people to explain things to.

Spoilers all of season 1 and 2.
Ship : Chuck/Sarah
A few minor changes to season finale.Bryce never asks Sarah if she's coming. Casey's team is never betrayed. Bryce lives and downloads the new Intersect and Sarah is his partner again .She went instead of speaking up because she panicked after seeing how hurt Chuck was when he walked off after she told him she was going to be assigned with Bryce. Basically she left because she thinks she only brings him pain. Bryce tries to make her his partner in romance again but she's not having it.
To the surprise of Bryce and the PTB (Beckman and any other superiors) the new Intersect team just isn't as effective as the one with Chuck on it in spite of Bryce's training and experience. If the new team runs across any one that Team Chuck worked with the difference gets commented on.
Meanwhile Chuck has managed to get a better job and is working on creating his own video game or other software or hardware(possibly collaberating with his father) . He also saves some peoples lives (either from spy world baddies or regular world ones) and gets some recognition for that .
After realizing that Bryce as Intersect is a failure (plus have some info about how Casey is still as effective as ever but he doesn't quite fit into his old world any more) Beckman decides that the old team has to reform. Maybe have Bryce and Chuck (pre and post download) tested to try and determine why Chuck's more effective than a trained agent.
Spoilers Up to and including most of Lethal Weapon.
Basically I want it to end up Chuck/Sarah but I want him to withdraw drastically because of the way she behaved around Cole Barker. And for his withdrawel to lead to the Sarah trying to fix things and making an obvious effort to have something with Chuck that gets noticed by Beckman (because I don't get why she was worried about Sarah being compromised from what she saw Chuck do).THe only part of lethal weapon I wold change would be an add on to Chuck's speech. POssibly something about him having that life back and getting that girl while Sarah would get the regualar spy life back.