In the first Resident Evil, Umbrella created the world's first true Artificial Intelligence. And in the RE Universe, you can drop the word "Artificial" and that sentence would still be true. Umbrella builds a viral research lab to develop and perfect their zombie formula (because they know what the consumer really wants: The Undead) and of course they do so directly under a civilian population center. In perhaps the only rational decision ever made by Umbrella, they realize they really shouldn't be in charge of anything, and develop an advanced AI to put in control of it instead. But when the shit hits the fan (as is wont to happen when you build a shit factory right beneath Fan City,) the AI does its job and seals the lab to prevent further casualties. Umbrella's response to their program doing exactly what they built it do was, for some reason, to send a security team in to override the whole god damn thing. Then, after the first team is murdered by the murder machines they built in the murder factory (that at this is point is totally sealed off, remember,) they send another. They make it very clear they will just keep sending teams into the "Pit of Bad Idea" until everyone on the entire planet is dead, and by the third film, they actually manage that.
But despite what the entire running time of Resident Evil tells you, there was only one protagonist in that movie: Not the sassy Latino, not the tough as nails black guy, not even Milla herself - no, the only good guy in that movie is The Red Queen supercomputer (the "evil" Artificial Intelligence from above.) She's literally the only one, anywhere, that thinks perhaps unleashing the zombie death-plague is just maybe not the best idea. If she has a failing, it's only that she's the least user-friendly Graphical Interface since someone installed Windows 98 on a guillotine: She's a blood-red hologram of a creepy seven-year-old girl. She looks like the offspring of every Japanese horror movie raping each other, and while she's got enough supreme mastery over the entire laboratory complex to kill every single person who comes anywhere near it, they apparently forgot to give her so much as a twitter account to tell those people not to come near it.
For the purpose of determining exactly how stupid the human "protagonists" are by comparison, we've developed the Zombie Movie Intelligence Test. The test is simple: You count how many seconds pass between the first time our heroes see a zombie, until they shoot it in the head. Then you just subtract that number from 100 to find their IQ. Applying this test to Resident Evil, we find our heroes have scored a new world record: -1100 points. It takes the Umbrella employees an insane twenty minutes to rediscover headshots. They expend most of their ammunition (and half their team) in a single firefight, and they don't hit a head once. Never mind basic survival, that's statistically impossible. They hit the walls, the roof, the floor, and destroy the "safety controls" on the experimental mega-zombie containment units littered about the room, which releases even more undead; they shoot so badly they actually increase the number of zombies.
In fact, while every other zombie movie has the hero inevitably trying out a headshot when all else fails, our heroes have to be told pointblank that shooting something in the face might kill it. By the supposedly "villainous" supercomputer! They reward her sage wisdom by opening every compartment in the leaking viral weapons lab, releasing even more powerful super-monsters, ignoring her final pleas to at least leave behind the obviously infected soldier and not spread the plague to the outside world, and ultimately by killing her. So while most people came out of Resident Evil thinking they'd just witnessed a happy ending to a stupid, traditional action movie -- where the good and noble soldiers triumph over an evil computer -- Resident Evil is, in fact, the first post-modern nihilist action movie: The world is ultimately destroyed because everybody ignores the hero for the entire movie, until they finally just kill her.
In RE: Apocalypse, Raccoon City is now a zombie-infested wasteland, Umbrella have sealed off the entire city and decided that this is the perfect time to deliberately unleash two more unstable experiments. Presumably on the grounds that they can't make things any worse, and just like their company motto says: They're wrong again.
Umbrella genetically upgrade the protagonist from the first film (Milla) to become a perfect assassin, on the grounds that she's already betrayed them in the previous movie, vowed vengeance upon them after they kidnapped her generic love interest to turn into a monster, and also because they all got their PhDs in Retardology. This mutated love interest is the crux of Umbrella's role in the second film, as he roams the city stalking Milla. So what's Umbrella trying to accomplish here? Even they don't seem to know: The entire experiment (the "NEMESIS project") apparently only exists in the first place to test if a surgically mutilated environmentalist can win against civilian peace officers when he's equipped with impenetrable body armor, a Gatling gun and a rocket launcher. To which the answer is "Of course, assholes." You do not need mutated super-strength to pull the trigger on a bazooka: WE HAVE THOSE NOW. PEOPLE USE THEM.
Ultimately the former love interest catches up to Milla, and Umbrella force a mixed martial art competition between the two - complete with ring and stage lights (yes, they actually import stage-lights into the middle of a city of brain-dead beasts, to better recreate the pay-per-view event this "scientific process" was based on). Because apparently "retarded killer attacking unarmed supermodel" yields important, relevant scientific data in the RE Universe.
SPOILER: Forcing your horribly mutilated secret weapon hippie to give up his weapons and fight his old friend works out even more exactly like you'd expect than you'd expect.