Here's a comprehensive list of the canonical issues in the bonus scenarios (the three main game scenarios are not included as they are horribly shortened and should not be taken as canon by anyone).
Beginnings: Works except for Wesker having to activate the cable car and fighting the Proto Tyrant (which are merely gameplay mechanics to stretch the level) and the opening cutscene. That one is almost an exact retelling of the
elevator cutscene from
biohazard 0. Some stuff was cut to shorten it, Birkin gets a little more angry and his voice actor now sucks (that guy's supposed to be 36 years old?).
Important new plot points:
- Sergei is on a mission to retrieve the T-A.L.O.S. from the Arklay Research Facility
- Sergei meets Wesker and is not pleased about his leaving the Management Training Facility behind, he seems to be one of the highly loyal kind
- After that encounter, Wesker regrouped with the S.T.A.R.S. Alpha Team and lured them to the mansion in the evening of July 24th, 1998
Nightmare: Works if Wesker has some sort of master key. That would mean that most of the doors were unlocked until the Alpha Team arrived at the mansion and Wesker locked the doors to hinder them from progressing too fast. Thus, it could be entirely possible that Rebecca got to the staff quarters and took a rest there.
Important new plot points:
- Rebecca and Richard saw Sergei and Ivan leaving the mansion area, with a bodybag that contains the T-A.L.O.S. prototype
- Richard was bitten while he was trying to save Rebecca from the Yawn
Rebirth: Now that's just a matter of preference. While that scenario clearly shows Wesker impaled by the Tyrant, I still like the story given in the
biohazard archives more. There, he died from a bullet wound and/or traumatic brain injury (when he was hit by the Tyrant) - that just works way better for me because it doesn't involve innards ripped out of Wesker. But as said, just a matter of preference.
Important new plot points:
- Wesker tried to get the Umbrella research data immediately after his rebirth
- Sergei transferred this data to the U.M.F.-013 in fear of Wesker attempting to steal everything
- Wesker's access privileges to the mainframe system have been revoked
- Wesker didn't know about Red Queen yet (seems to be a pretty secretive program, huh)
- There's also White Queen
- Red Queen has three objectives, of which only two are given: Management and protection of Umbrella assets as well as the protection of Umbrella officer lives
- Wesker meets Lisa one last time, who chases him through the Spencer estate before Wesker gives her the final treatment
Death's Door: Works if Ada survived being thrown at the panel in Leon B and bandaged herself.
Important new plot points (speculation in italics):
- Leon B is the canonical scenario
- Ada survives being thrown at the panel by the T-103 and bandaged herself
- She gets a tissue fragment from Birkin's seemingly dead body (fourth form) in the underground laboratory (
or, alternatively, just provides Wesker with "a different present", as she did in
biohazard4, I mentioned that possibility below), then gets back up to the train station and drops Leon the rocket launcher to finish off the mutated T-103
- Ada puts Sherry's pendant with the second G-Virus sample in her pocket, leaves the area through the sewers ("Death's Door" begins here) and gets back up to Raccoon City in order to meet a contact person at the Apple Inn
- She finds this person lying dead and moments later, Wesker tells her via phone that she failed and that her rescuing Leon will have consequences for their organization (he's most likely talking about S)
- Ada shows him the tissue sample after which Wesker informs her that Raccoon City will be sterilized by a missile in a few moments and her only way to get out is a chopper which an Umbrella officer (should be Sergei, but a picture of...someone else is shown) uses to escape from Raccoon City, and provides her with the grapple gun, thus "saving her life" through the information
- Ada wonders what the G-Virus getting out would mean if even the t-Virus had such devastating effects (which is kind of strange as the G-Virus works only through direct injection, but she either doesn't know that or means something else by "getting out") - she could have provided Wesker with a fake tissue sample but as they have a healthy relationship in 2004 and she still had the pendant to provide her own organization with a G-Virus sample, Wesker probably got the tissue fragment
- Ada makes it to a roof, defeats another Tyrant and uses her grapple gun to board the helicopter
- In the helicopter, Sergei Vladimir and another mysterious man (maybe this is
the first picture of Spencer...but the dialogue suggests something else) have a conversation
Sergei: You think I'm reckless, don't you?
???: You stole the computer core from your own company. I wouldn't exactly call that stable.
Sergei: (laughs) The people who go down in history as its heroes are never stable. Inside U.M.F.-013 is all of the research data. With that, Umbrella will rise from the ashes. (laughs again)
Fourth Survivor: Works except for the opening which is a retelling of the original
4th Survivor intro and the
BIOHAZARD 3 LAST ESCAPE epilogue file.
- The survival rate of the Umbrella Special Forces was 4% (so it consisted of 25 people, as only HUNK survived)
Dot: I saw a thread about that some time ago, on Capcom BBS. But I cannot find it anymore.