As the others have said, in game movies can be useful. Though I assume you would like an intro akin to the Future Tense or Babylon 5 Armada 2 mods?
If so, then there are a few requirements - you'll need software capable of rendering animation (3ds max, Maya, and Lightwave are three of them), an after effects suite (such as Adobe Premiere or the easier to obtain Movie Maker), audio editing software (audacity is the best I've found, and its free) and the Rad Game Tools. These are what you need in terms of software, I'd also recommend a fast graphics card (128 is good though 256 or above is ideal) to speed up rendering time as well as about a gig of RAM for the same reason.
Then it comes to the animating. This seems a lot easier than modelling though to create long timed animations that play fluidly and don't seem to be unnatural takes a lot of practice.
Your best bet would be to get a trial version of Maya if there is one, learn the ropes over thirty days and then get the Trial of Max to do the actual animation. After this max can be obtained for later usage.
Rambled on for a bit I think
Seriously though, good luck in this. A mod with a specific story or a crossover really needs a new intro, the old ones simply confuse the player in the long run. Just stick with the programs and take little steps, don't try to make the whole thing in a day. Better to spend more time perfecting the scenes than making the whole thing suffer due to a crowded schedule.
If any help with anims are needed, I'm here and there are people many factors of ten times more skilled than me at sci-fi meshes.