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In Resident Evil: Apocalypse (the second film, from 2004) the zombies get nuked, but there are zombies reappearing in the 3rd, 4th and 5th films. How did they survive?

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The honest answer can be found at BoxOfficeMojo:

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"Resident Evil" is one of the oddest film series because it's actually gotten bigger box office over time. PT Anderson may have been thinking the second film would be it, and so destroyed the zombies, only to find that $129M wouldn't be ignored.

And the more successful they are, the more freedom he gets and, hey, getting paid millions or tens of millions, even, for hanging out with your wife might not be a bad deal, especially if your wife is Milla Jovovich.

Continuity is not a big thing in these movies however. It's not Friday the 13th level of incoherence, but it's not great.

If you need an "in-universe" explanation, the simplest one I can think of is this: The breakout wasn't limited only to Raccoon City. As a result, even though the zombies there were destroyed, Umbrella Corp was busy making them all over the world. This is actually borne out, as a theory, by one of the opening scenes of RE5 (Retribution), where the outbreak appears to have started in Tokyo. (So, not Raccoon City.)

Later, Alice visits the scene in some kind of holodeck, which you can see on YouTube.

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    Well, it seems it's all coming to an end now... I hear this next one will be the last :P – Catija Aug 10 '16 at 22:27
  • If it makes money, they'll either talk Anderson/Jovovich into doing YAS (yet another sequel) or they'll reboot it with someone else. It's basically free money. They hate leaving that stuff on the table in H-wood. – moviegique Aug 10 '16 at 23:07
  • Truly horrible film series. Kinda sad that it makes so much money. This is 100% the answer to all questions regarding plot holes in the series, and there's a lot of them. This film series is the movie version of a low quality fast food restaurant. – Tom Aug 12 '16 at 16:35
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    @Tom - I know deep down i agree with you. But DAMN! I sure love tucking into a piece of Resident Evil, just like I love tucking into the odd cheeky Big Mac or Bucket of KFC. It's good to turn your brain off for a bit and just enjoy big explosions and flashing things. – Cearon O'Flynn Feb 7 '17 at 15:45

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