I picked this tidbit up from another forum:

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This is the best summary I've found about what's going on with HR 3997

Anyway, if you're scratching your head about how the bailout legislation, which was conceived over the weekend, ends up numbered H.R. 3997 when they're already well into the 7000s with House bills already (they're numbered in order of their introduction), the answer is that they're going back to a trick we've seen them use before -- taking an old bill that has passed one House but not both, and hollowing it out and replacing that text with the new stuff.

So H.R. 3997, an old tax bill that passed the House, bounced back and forth a few times after being amended, but was never passed in the same form by both houses, which means it's still available as a legislative vehicle. That means that technically, what's under consideration in the House today is an amendment to the Senate amendment to the House amendment to the Senate amendment to H.R. 3997.

Seriously.

Why? Because pretending that the bailout package is just a new amendment (in the nature of a substitute) for what now stands as the old body of H.R. 3997 means they can get expedited consideration on the House floor, plus be protected from a Republican motion to recommit [send back to committee, essentially killing the bill].