by the looks of it I'd say most all of it was AE, with some plug ins. AE has very powerful 3d space capabilites, and if you notice the elements are all 2d.
the part where it is flying through the inside of whatever.... that was is just a repition of a layer in 3d space with a hole in it and the camera is flying through it.
no doubt that took a while to make though.
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"I'm glad that in our endless pursuit to be three years behind snowboarding, we've finally gotten around to their FAG phase." -Micah Abrams