* If something radically altered your DNA, the first place the changes would show up would be at the site of a wound, where cells are dividing rapidly and new tissue is being produced. What's the first part of William Birkin to mutate dramatically? His right arm, which was riddled with bullets during the laboratory break-in. In addition, Birkin only changes forms after you fight him; he gets more alien every time he heals.
* It seems a bit odd that, when trying to start up the train in the B Scenarios, the game requires you to pick up two Joint Plugs and then immediately use them one room later, with nothing in between. Even more odd is that you only have to use one of the plugs on the generator - it automatically places the second one in with the first - when every other part of the game has you use items individually. Odd until you realize that what the game is doing is forcing you to have two inventory slots open, so that you can pick up the two-slot rocket launcher [[spoiler:Ada]] throws to you during the [[spoiler:Mr. X/Tyrant]] fight that starts immediately afterwards.
* As pointed out in a fan FAQ, the reason why HUNK's team attacked Birkin's lab in the first place was revenge for Wesker and Birkin stealing credit on the Nemesis project from the French branch of Umbrella by producing a viable sample in Lisa Trevor. With Wesker gone, Birkin was vulnerable and he had a shiny new virus that was ripe for the taking. This is proven by HUNK's CO being the R&D chief of the French branch, as well as certain details from the Wesker Report.


* Chief Irons has a pack of acid grenade rounds in his TortureCellar. At first glance, it may seem like they're there just for gameplay reasons. But think about what that room was used for, as well as the other chemicals such as chloroform and god knows what else. It's possible that Irons was secretly stealing acid rounds from the armory and using the sulfuric acid to torture people or break down their bodies ''Series/BreakingBad''-style to hide the evidence. How did he manage to get the acid out of the grenades without blowing himself up? In the remake of the first game, Barry refers to acid rounds as a "can of fizz" so maybe there's a way to easily open them up.
* Speaking of the Chief, what happened to the mayor's daughter's corpse? Obviously, he took it with him when he retreated to his torture cellar, but it's not there either when you enter it.
** The most logical answer is that he didn't feel like preventing her from turning into a zombie, and proceeded to wander from the torture chamber either into the police station or the sewer.
* William Birkin injected himself with the G-Virus, knowing full well that the virus could drive him to hunt down his own daughter and [[{{Squick}} inject her with mutated embryos.]] [[SarcasmMode Father of the year, people!]]