Street Fighter Alpha 3 first starts off with Bison tracking down Ryu and confronting him, then attempts to brainwash Ryu into giving into Psycho Power. Ryu has an inner conflict with himself on whether to give in, similar to his conflict to give into satsu no hadou. At any rate, he does give in, though it's important to note that brainwashed psycho power Ryu is not the same as Satsu no Hadou Ryu. Anyways, Ken and Sakura coincidentally arrive just at the same time as Sagat arrives to see Ryu again.

Sagat, who has regained his honorable warrior spirit since confronting Dan in SFA2 is infuriated when he sees how low Bison stooped Sagat fights Psycho Ryu while Ken and Sakura fought Bison. Sagat beats Psycho Ryu and then, judging by the game, Ryu managed to break out of his brainwashing and knock Bison away, forcing Bison to retreat. That ends Ryu's main portion of the story.

The next main character of SFA3 could be considered to be Cammy, since she has a huge plot around her in SFA3. This one most likely happened after Ryu's part of the plot (possibly a rather large amount of time), and basically involves how for reasons she can't figure out, Shadaloo decided to terminate her. This probably happened around the same time as Rose's portion of SFA3's plot; even though the two characters' plots don't interlap too much, Rose's fight with the Dolls in the game as indirectly indicates this, though of course I'm not sure and it really doesn't make too much difference either way (Rose can be considered a semi-main character of SFA3. At any rate, Cammy encounters Vega and probably Juli and Juni (judging from her in-game storyline) during this period and they were all sent to terminate her in some fashion. However, somehow, she managed to convince Juli and Juni as well as all the rest of the Dolls how they were truly expendable to Bison, and so all thirteen of the Dolls turned on Bison. In the process, they were all almost killed. Anyway, Bison was finally forced to retreat once again, and Cammy made her way to the Psycho Drives to use them to save the rest of the Dolls.

Finally, the last main character of SFA3 is Guile. His story had to had happened last in SFA3 since it's the one that finally ends Bison by blowing him and Shadaloo up. Basically, Guile catches up to Charlie and Chun-Li, then finally decides to join them and together the three take down Bison for good in SFA3 (though he would come back for SF2). Charlie and Guile confront Bison in the Psycho Drive room of Shadaloo headquarters and Charlie sacrifices himself to hold off Bison while the entire base
explodes.

Street Fighter Alpha 3 Boss Battles

The first character is the one you play as when that battle takes place

For example, if it says

"Ryu vs Sagat"

It's talking about the (mid)boss battle with Sagat you fight while you play as Ryu.

A note about the final boss battle with Bison: nearly all of these probably didn't
happen. The only confirmed ones to fight Bison are Ryu (sorta), Sakura with Ken, Rose, and all thirteen Dolls (it's possible that Cammy's battle with Bison took place right after all other twelve Dolls fought him, or that Cammy arrived in the middle of it to help them out, too. Juli's ending shows this a little, too, since Cammy arrives as Juli is fighting Bison or right after Juli loses consciousness to him or what have you), all of which Capcom has officially stated happened.

Adon vs Ken - Pointless filler battle and thus probably did not happen.

Adon vs Rose - Pointless filler battle and thus probably did not happen.

Adon vs Bison - Bison challenges Adon for the hell of it. Like all boss battles with Bison in SFA3 besides the confirmed ones, this did not happen. ...damn, even Adon's SFA3 ending is pointless (he's searching for Akuma in SFA2, he's still searching for Akuma by the end of SFA3).

Akuma vs Adon - Adon finally finds Akuma. If this battle happened, it happened after Adon's storyline search for Akuma when you play as Adon, obviously. Whether it actually happened or not, regardless, who knows? Adon himself is left on a non-definately-resolved plotline, there.

Akuma vs Guy - Guy wants to stop Akuma from seeing Bison for some reason. Well, Capcom did state that Bushin was opposed to Akuma because Akuma disrupted the flow of nature for some reason, but I'd be surprised if this fight happened.

Akuma vs Bison - Bison challenges Akuma for the hell of it. Like all boss battles with Bison in SFA3 besides the confirmed ones, this did not happen.

Balrog vs Gen - Balrog lays the beatdown on Gen for beating up Shadaloo members. This fight probably just exists because Capcom wanted to show more in-game about how Gen knew about Shadaloo and beat up its members while looking for worthy opponents, which is official statement. This particular battle with Balrog, however, most likely did not happen.

Balrog vs Birdie - Balrog finds out about the Psycho Drive from Birdie. Pretty important to Balrog's ending. This battle probably happened due to that, assuming how much you care to think Balrog's ending is canon in any form.

Balrog vs Bison - Balrog challenges Bison and demands for the Psycho Drive. Officially did not happen. Capcom has officially stated that Balrog never got the chance to betray Bison in SFA3, which is why he's still a member of Shadaloo in SF2.

Birdie vs E. Honda - Pointless filler battle and thus probably did not happen.

Birdie vs Blanka - Pointless filler battle and thus probably did not happen.

Birdie vs Balrog - Bison sicks Balrog on Birdie. Real way it happened is probably Balrog vs Birdie above.

Birdie vs Bison - Birdie challenges Bison and demands for the Psycho Drive. Like all boss battles with Bison in SFA3 besides the confirmed ones, this did not happen. His own ending where Chun-Li and Charlie arrest him at the Psycho Drive gets in the way of Guile's ending which officially happened, so Birdie's own ending definately didn't happen. The real way his search for the Psycho Drive seems to have gone, if it occurred at all, is Balrog's ending (without attributing the psycho drive's destruction to Birdie and Balrog, just like everyone else's ending that involves destroying it besides Guile's), and thus I highly doubt he ever confronted Bison in SFA3.

Blanka vs Dan - A 'for-fun' battle that is a large basis of Blanka's SFA3 storyline, which doesn't contradict with any other storylines once you get rid of the destroy Bison and psycho drive aspects, etc, and thus probably did happen.

Blanka vs Zangief - Pointless filler battle and thus probably did not happen.

Blanka vs Balrog - Pointless filler battle and thus probably did not happen.

Blanka vs Bison - Bison challenges Blanka to make into a guinea pig. Like all boss battles with Bison in SFA3 besides the confirmed ones, this did not happen.

Cammy vs Dhalsim - Dhalsim notices that Cammy is beginning to develop her self-conscious. This battle might have happened. Not really too important either way, but I do lean towards it happening since there's nothing else that Dhalsim really gets to do in SFA3.

Cammy vs Vega - Vega has been sent to investigate on Cammy. This battle definately did happen, since it's important to Cammy's and Vega's storylines that have been officially stated to have happened in SFA3. Cammy won this battle (she had to in order to reach and fight Bison, which also officially happened), but Vega's dialogue indicates that he purposefully threw the match.

Cammy vs Juni and Juli - A seemingly pointless filler battle, but it most definately did happen, as shown by Juli's storyline. Odds are this is when Cammy met with the other Dolls to get them all to fight against Bison, which officially did happen.

Cammy vs Bison - Bison decides to finally exterminate Cammy, personally. This battle officially happened, with some added bits from official statements. Capcom has stated that all thirteen Dolls rebelled against Bison together, so Cammy almost definately picked up Juni and Juli from her battle with them.

Charlie vs Cammy - Charlie apprehends Cammy. Mere existance of it contradicts Cammy's storyline, which did happen, and Charlie's ending generally didn't happen, so all evidence points to that this battle
didn't happen.

Charlie vs Rolento - Capcom officially stated Charlie never met Rolento. ....wow, this battle again? Oo Why does Capcom keep making Charlie fight Rolento if they never officially meet in the actual official storyline? Well, guess there's no other "corrupt army soldier" character that Capcom has, but this battle didn't happen.

Charlie vs Bison - Didn't happen in the form that playing as Charlie portrays it in. The true way it happened was Guile's storyline. ....why does Charlie always get the what-if storylines when you play as him? Strange.

Chun-Li vs Birdie - Chun-Li gets information from Birdie about where Shadaloo's base is. Actually, this battle might have happened. There's no indication that Chun-Li arrested Birdie here, so Birdie could continue his own storyline, and also, Birdie tells Chun-Li that he has business in Thailand, which is probably him seeking out the Psycho Drive. Of course, there IS the fact that the entire rest of Chun- Li's SFA3 plot when you play as her did NOT happen...

Chun-Li vs Cammy - Cammy attacks Chun-Li in the name of Bison. Didn't happen. Chun-Li's battles and ending from here on when you play as her completely contradict Cammy's official storyline, that did officially happen, in SFA3.

Chun-Li vs Juli and Juni - Juni and Juli attack Chun-Li in the name of Bison. Didn't happen for the same reasons as Chun-Li vs Cammy.

Chun-Li vs Bison - Chun-Li finally finds Bison and fights him to get him to stop using poor underage girls like Cammy, Juli, and Juni. Chun-Li's real SFA3 story is when you play as Guile. This did not happen.

Cody vs Birdie - I dunno. Dialogue indicates that Birdie is representing a generic Metro City thug, here, and not Birdie from England. At least... I can't figure out why else Birdie would say "You used to be something around here." Since when did Cody travel to England to bust heads, there? Oo

Cody vs Guy - Guy tries to reform Cody. Final Fight One dialogue shows that this battle did happen.

Cody vs Bison - Cody attacks Bison for the hell of it >:} LOL, I personally like how Cody just wants to get into tons of battles just for the hell of it because he's addicted to fighting! This is generally a pointless filler battle that thus, like the majority of SFA3 battles with Bison, did not happen. Guy never got that close to Bison, anyways, so the majority of Cody's ending up until the destruction of Bison most definately didn't happen (though Guy wanting to reform Cody definately did, as shown by Final Fight One dialogue).

Dan vs Chun-Li - Hilarious joke battle, but not really any story relevance, and Blanka's storyline seems to be the true way Dan's storyline played out in SFA3, so I don't think this one happened (or any of Dan's SFA3 boss battles when you play as him, for that matter).

Dan vs Sagat - Sagat is annoyed that Dan's pestering him again and Dan offers to teach Sagat Saikyo style. I'd be surprised as heck if this battle happened. I don't see why Sagat would purposefully lose to Dan TWICE.

Dan vs Balrog - Pointless filler battle and thus probably did not happen.

Dan vs Bison - Like all boss battles with Bison in SFA3 besides the confirmed ones, this did not happen.

Dee-Jay vs Adon - Pointless filler battle and thus probably did not happen.

Dee-Jay vs Sagat - Ditto. While the previous one led into this one, neither are important to Dee-Jay's overall SFA3 plot at all.

Dee-Jay vs Bison - Ditto once again.

Dhalsim vs Rose - Dhalsim tries to convince Rose not to rush into things. Might have happened. Dunno. Most of Dhalsim's tenure when you play as him seems... iffy, though.

Dhalsim vs Birdie - Dhalsim reads Birdie's mind to find out location of Shadaloo hideout. Probably didn't happen, since Dhalsim never got very close to Shadaloo at all during SFA3.

Dhalsim vs Juni and Juli - Ditto. Pointless filler battle.

Dhalsim vs Bison - Ditto.

E. Honda vs Ryu - E. Honda and Ryu fight for fun. This battle happened. It's referenced in Sakura vs E. Honda.

E. Honda vs Sodom - E. Honda and Sodom meet up again. This battle might have happened. Probably did, but not important either way. It's another fun reunion or something.

E. Honda vs Bison - Like all boss battles with Bison in SFA3 besides the confirmed ones, this did not happen.

Evil Ryu's boss battles (Sagat, Bison, Shin Akuma) - Like SFA2 Evil Ryu, Evil Ryu's tenure when you play as him is officially entirely what-if, and this battle did not happen.

Fei Long vs Balrog, Vega, and Bison - Everyone tries to get Fei Long to join Shadaloo. While Shadaloo might have been seeking Fei Long, they officially weren't trying THAT hard with that many marquee men going after him, so those fights didn't happen.

Gen vs Ryu - Gen and Ryu fight for the heck of it. Actually less pointless filler than that description gives. Here, Gen comments about how Ryu using a toned down version of Ansatsukan and how he can sense the power within him. Dunno if it happened but wouldn't be surprised if it did.

Gen vs Akuma - Gen finally gets his deathmatch with Akuma. ...well, not sure if it was to the death, or if it happened in the form that is portrayed here.

Gen vs Bison - Bison and Gen fight for the hell of it. Pointless filler battle that,
like many battles with Bison in SFA, did not happen. The important thing to Gen's storyline was the battle with Akuma.

Guile vs Chun-Li - Chun-Li tries to stop Guile from going after Charlie. Pretty important to Guile's storyline in SFA3, which officially happened, so this battle almost definately did happen.

Guile vs Charlie - Guile finally finds Charlie. Officially happened.

Guile vs Bison - While Guile's ending happened, I don't believe Capcom has stated whether or not Guile had to fight Bison to get Bison to retreat to the base, or if Guile and Charlie just infiltrated Bison's base without having to fight Bison first.

Guy vs Karin - Karin tells Guy of the Bushin prophecy that Guy will rise against Bison. ...ironically, that prophecy turns out to be false. Real false. Guy's true SFA3 storyline is officially what happened with him in Rose's storyline, so I'd be surprised if any of his boss battles happened.

Guy vs Gen - More about the Bushin prophecy, really. Ditto.

Guy vs Bison - Definately did not happen. Even Zeku's prediction that Guy would fight Bison ended up being wrong, since he officially never got that close to Bison in SFA3 (his true SFA3 ending was Rose's) and dissappeared after that. Hmm. ...unless they meant Guy would fight Rose (who takes Bison's place for a bit or more, as shown by her ending) or something, but in that case, Rose probably killed him (see Guy's section in the miscellaneous characters section)

Juli [Noembelu] vs T. Hawk: See T. Hawk vs Juli [Noembelu], below. Noembelu is in brackets because it's officially the Doll Noembelu that T. Hawk knew and thus that he recognized and all. I don't really think this battle happened, though, but I could be wrong. Capcom hasn't stated anything, here, besides that T. Hawk's after Noembelu and not Juli in SFA3.

Juli vs Cammy - Juli finally finds her target. Almost positively happened, as shown by Juni and Juli together going after Cammy when you play as her (which also indicates that odds are very high that Juni was officially with Juli the whole time. Those two really don't split up very often, but the game's arcade mode storyline doesn't let you dramatic battle play as both for obvious reasons).

Juli vs Bison - Bison decides to finally exterminate Juli, personally. All thirteen Dolls did fight against Bison together, but dunno if it was like the game portrayed, here. The game when you play as Juli indicates that Juli lied to Bison about killing Cammy, then Bison decided to kill her anyway, which caused her self-defense instinct to kick in. After that, I suppose Cammy (and the other Dolls, if they weren't with Juli already) came along to help her fight Bison. Well, it's shown by Juli's ending that Cammy came along later to help her out, but dunno. All there really is regarding official statements in this matter is that all thirteen Dolls turned against and fought Bison together.

Juni vs E. Honda - Juni fights E. Honda. Did she learn about Ryu's location from him? Is Juni seeking out Ryu even canon at all? Dunno.

Juni vs Ryu - Definately didn't happen. As per official statements, Ryu would fight Bison, himself, so Juni obviously didn't get to fight and beat him.

Juni vs Bison - Bison decides to kill Juni after she beats Ryu. Definately did not happen in this format. The real way Juni's fight with Bison occurred is with all the other Dolls, as shown by Juli's and Cammy's storylines. The evidence highly points to that Ryu's SFA3 tenure took place significantly earlier than the Doll storyline.

Karin vs Blanka - Pointless filler battle and thus probably did not happen.

Karin vs Sakura - Might have happened, but dunno. Karin admits after it that Sakura's still better, so it's not like it shifts storyline tiers at all or anything even though Karin wins this match. I think it did happen, myself.

Karin vs Juni&Juli and Bison - Like all boss battles with Bison in SFA3 besides the confirmed ones, this did not happen. This includes the Juni and Juli lead-up battle.

Ken vs Karin - Ken and Karin have a fun and happy conversation about Sakura. Actually probably did happen due to the two characters' connection about knowing other, even if it's not too important to the overall story.

Ken vs Sakura - Before Bison shows up, Ken finds Sakura in Thailand ready to meet Ryu. Almost positive this happened, since it coincides with the official statement that Ken and Sakura fought Bison together after finding Ryu under his control.

Ken vs Bison - Bison challenges Ken for the hell of it. It happened, but not really like this format at all. The real way it did is officially with Sakura and had more to do with Ryu than this, and thus probably more like Sakura vs Bison, below.

Bison vs Akuma, Ryu, and Sagat - Bison gets a what-if storyline where he destroys the world. These fights obviously did not happen in this form. His brainwashing of Ryu itself happened in a different way, as per official statements. Bison's real SFA3 storyline basically involves him being all the villain of the main characters of SFA3 (Ryu, Cammy, Rose, and Guile).

R. Mika vs Karin - Karin decides to sponsor R. Mika if she ever becomes a pro-wrestler. May or may not have happened. Dunno.

R. Mika vs Zangief - R. Mika finally gets to meet Zangief. May or may not have happened. Actually probably did, but it's not a big deal either way.

R. Mika vs Balrog and Bison - Like all boss battles with Bison in SFA3 besides the confirmed ones, this did not happen. This includes the Balrog lead-up battle.

Rolento vs Sodom - Sodom tells Rolento that he's lost site of his ideals. This battle is important to Rolento's storyline (which I'm pretty sure happened, since after removing the Psycho Drive destruction like you should with all SFA3 storylines besides Guile's, it doesn't contradict anything and is definately not just filler for Rolento), so this battle definately happened. It's confirmed by Street Fighter Eternal, pretty much.

Rolento vs Cody - Rolento tries to recruit Cody, but then sees what Cody has become and decides not to. This battle is onfirmed by Street Fighter Eternal.

Rolento vs Balrog and Bison - Like all boss battles with Bison in SFA3 besides the confirmed ones, this did not happen. This includes the Balrog lead-up battle.

Rose vs Guy - Guy wants to follow Rose, but she won't let him. Important to Rose's ending, which did officially happen, thus this battle/meeting definately happened.

Rose vs Vega - Vega tells Rose that he doesn't understand why she's so suicidal. This ending probably happened. A lot of the 'Doll storyline participants' seem to criss cross paths a lot, and this would be no exception.

Rose vs Juli & Juni [Aprile?] - Rose fights some of the Dolls that Bison sTicks on her while he waits for someone else to arrive (most likely Cammy, but it might have been Ryu. I lean more towards Cammy since Rose in general is more involved with the Dolls than Ryu, and her meeting with Vega as well as this Juli & Juni boss battle implies that her storyline takes place at the same time as Cammy's, which takes place after Ryu's does). The actual battle was probably fought with Aprile, since J&J were most likely
pursuing Cammy at the time and Capcom officially stated that Aprile's brother went to see Rose at the beginning of SFA3, so Aprile would be the one that's most storyline significant to Rose.

Rose vs Bison - Rose finally reaches Bison. This battle officially happened.

Ryu vs Rose - Rose warns Ryu about Bison. This battle probably happened since it's semi-storyline significant.

Ryu vs [Psycho] Ken - Ryu comes across Psycho Power Brainwashed Ken. This battle officially did NOT happen and Capcom has directly stated as such, and also stated that Psycho Ken never happened. The real one who got brainwashed was officially Ryu, himself.

Ryu vs Bison - Bison challenges Ryu to brainwash and control him. Happened, pretty much, though you need to take into account Ken and Sakura's battle with Bison and how it fits in, too. Basically, Ryu fought Bison, got brainwashed as per his ending, then... well, it continues into Sagat's, Ken's, and Sakura's storylines there. ...actually, Ryu's ending contains Ken's role in that particular arc of the SFA3 storyline, too

Sagat vs Dan - Sagat fights Dan and sees the rage in Dan's eyes. It reminds him of the rage he feels. This battle is just a re-showing of Dan's SFA2 battle with Sagat and thus obviously did happen. Although the game only implies it a little by the way Sagat feels after the battle, officially, Sagat let Dan win this battle.

Sagat vs [Psycho] Ryu - Sagat is mad at Bison for stooping so low as to brainwash Ryu. Happened. Capcom officially stated that Sagat fought Psycho Ryu while Ken and Sakura fought Bison.

Sagat vs Bison - Didn't happen. Officially, Ken and Sakura handled Bison while Sagat handled Psycho Ryu. ...well, okay, Sagat did stand up against Bison a little as Ryu began to break out of his own brainwashing, but that's more Sagat's ending than this particular boss battle against Bison.

Sakura vs E. Honda - Sakura learns (generally speaking) from E. Honda where Ryu is. Probably happened.

Sakura vs [Psycho] Ryu - Sakura finds Ryu brainwashed by Bison! While she did find out about that, she didn't officially fight Psycho Ryu. Sagat did. As per official statement by Capcom, Sakura, meanwhile, fought Bison along with Ken.

Sakura vs Bison - Sakura fights to protect Ryu from Bison. Happened, though Ken was with her to help. Too bad Capcom couldn't make this dramatic battle to show it better. It wasn't until the Dreamcast version of SFA3 that there was a fully working Dramatic Battle mode, and Capcom probably wouldn't let the player fight dramatic battle style in arcade mode just for storyline reasons, anyways, since arcade mode is supposed to be solo.

Sodom vs Rolento - Rolento demands that Sodom join him. Happened, though the more accurate version is probably Rolento vs Sodom above, since Rolento's storyline isn't as much of a joke ending as Sodom's.

Sodom vs Chun-Li - Another thing that indicates that Rolento's version is the real way things happened, instead of Sodom's, is the fact that Sodom's storyline has boss battles like this, which definately didn't happen. (Battle was pointless filler with Chun-Li trying to stop Sodom because it was her job to go after Shadaloo and she didn't want him to get in the way or so)

Sodom vs Bison - Like all boss battles with Bison in SFA3 besides the confirmed ones, this did not happen. Sodom's storyline when you play as him on a whole apparently is what-if, with Rolento's being the true version.

T. Hawk vs Charlie - Charlie warns T. Hawk about Bison. Might have happened, though I'd be pretty surprised if it did.

T. Hawk vs Juli [Noembelu] - Officially, Noembelu was the Doll T. Hawk was seeking, not Juli. Here, he finds her. Might have happened, but I don't think so cause it doesn't seem to fit in with all thirteen Dolls betraying Bison together.

T. Hawk vs Bison - T. Hawk fights Bison to free Noembelu. Like all boss battles with Bison in SFA3 besides the confirmed ones, this did not happen. ...how canon T. Hawk's tenure when you play as him in SFA3 is really rather up in the air right now.

Vega vs Zangief - Zangief attacks Vega for being a member of Shadaloo, though Vega denies that he is since it's not supposed to be a publically known fact. Actually, I'm inclined to believe that this battle did happen, since Capcom shows that Zangief knows about Vega in Zangief's SSF2T ending, where he's making fun of a picture of Vega.

Vega vs Cammy - Vega finally finds Cammy, but also finds that he's realizing she's more than just a mere experiment. This battle did happen, since it's important to Vega's ending which officially happened, and this is Vega's point of view on it. See Cammy vs Vega above for more information.

Vega vs Bison - Vega argues with Bison about Cammy. While the argument might have happened (which would be another thing that leads Vega to decide to betray Bison indirectly by saving Cammy), Capcom has officially stated that Vega never actually betrayed Bison (besides saving Cammy, which Bison didn't know about) or fought Bison, which is why Vega's still a member of Shadaloo in SF2.

Zangief vs Rolento - Pointless filler battle and thus probably did not happen.

Zangief vs Chun-Li - Ditto.

Zangief vs Bison - Like all boss battles with Bison in SFA3 besides the confirmed ones, this did not happen. ...Zangief didn't really get to do much during SFA3, officially.