WMG / Resident Evil 0

Billy knows more than what he told Rebecca

When you reunite with Billy Coen in the water treatment facility in the final quarter of the game, he spots some nearby corpses and mutters to himself about Marcus "experimenting with the mother virus", whilst having a quick flashback to scenes of massacred Africans. Resident Evil 5 reveals that the "mother virus" and the Progenitor virus are the same thing; the original viral strain recovered from the sacred site of an African tribe by Spencer, Marcus and Ashford. Further, because the virus only propagated itself there, Umbrella had to fight a continuous battle against the natives to push them away from their land so they could harvest samples. Maybe Billy's unit was actually involved in suppression actions against that tribe and he made up the guerrillas story to make himself look more sympathetic?

Wesker and Birkin just pretended to be rivals in order to prevent Marcus from getting suspicious and/or paranoid about them.

One of the diaries in Resident Evil 0 notes that the two are very competitive, yet they seem to be perfectly willing to cooperate in containing the T-virus outbreak during the game itself, and Birkin's letter to Wesker at the end of REmake is pretty friendly. Since they apparently also cooperated on Marcus's assassination, it's apparent they intended to usurp his position from the beginning, and pretended to be rivals to prevent the idea from ever entering his mind.

• I don't think they ever had to. The diary just said that Marcus wanted them to be rivals and that the Assistant Director (or whoever the fuck that was) should try to get on that shit, but it never said anything about it actually working. I mean, they might be competitive, but considering that Wesker didn't snap Birkin in half at some point, it was probably more of a friendly rivalry than anything else.

Umbrella builds many of its laboratories in the same style.

It would explain why Rebecca and Billy can visit an area that looks like the entrance of Birkin's lab in Resident Evil 0.

• That is the entrance to Birkin's lab.
  • Yet it's just thrown in at last moment as a reference to RE 2, and the game was originally meant to go from Marcus's lab straight to the Water Treatment Plant. Given that it's a last minute thing with not much thought behind it, it also doesn't add up with the geography. The part with Birkin's lab in RE 0 is basically a non-canon easter egg.
• Though that would explain why the Foyer in Marcus's headquarters looks nearly identical to the foyer of the original Mansion.
• Pretty much confirmed in the files of R Emake. Spencer hired Trevor to create the Mansion, and probably the style used inspired all the other facilities.

Rebecca reunited with Billy sometime after the Raccoon City incident.

• ...and settled down with him. It may be the reason neither of them has been seen, or heard from since.
  • Jossed by Resident Evil: Vendetta. By 2010^note which is post-RE6, she's a college professor and still canonically single.

The Leeches are actually the ones in control of Marcus

• Take a look at his face when he transforms into the leech queen. He is taken by surprise mid-laugh, throws up and has a look of shock on his face while he transforms. There are actually two minds; Marcus's mind, and the leech hive mind that allows him to exist. He thinks he is in control but they can take over at any time.

Billy was going to be invited into the U.B.C.S

Resident Evil 3: Nemesis lore states that the Umbrella Biohazard Countermeasure Service are predominantly made up of war criminals and death-row inmates, to ensure both suitable skills & morality and a viable source of leverage. If the transport hadn't been attacked, Billy would probably have been offered membership in the U.B.C.S as an alternative to the lethal injection.