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I've read that the first two movies are recaps of the series, and the third movie is a sequel to those two movies (obviously). But does this mean the third movie continues the story from where the series ends? Or is it an alternate ending? Or a spin-off? Or does it reveal more events from the series timeline?

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The exact placement of the Rebellion movie with respect to the series is still not entirely clear. This is what we know, though:

  • The movie is set in the final timeline - that is, the one depicted in episode 12, in which Madoka exists as a force of nature that eliminates all witches.
  • The movie occurs a while after the last pre-credits scene of episode 12 (the one where Homura tells Kyuubey about the previous timelines, in which witches existed, and in which magical girls had a more adversarial relationship with Kyuubey). The movie starts an indeterminate amount of time after this scene, though Kyouko, Mami, and Homura all look essentially the same, so it's unlikely more than a year or two has passed.
  • The movie is to be taken as the canonical continuation of the TV series (and, equivalently, the first two movies), so that it is the ending of the series (for now), not an alternate ending or a spin-off.

What is not clear:

  • We don't know how the events of the movie relate to the post-credits scene of episode 12 (果てしなき戦い / "The Endless War", discussed in this question), in which Homura sprouts witch-looking wings as she battles a number of wraiths in a wasteland. This scene could occur before or after the events of the movie - there just isn't enough information to tell at this point.

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