The short answer to this is that it flies out the window and is lost. This is a very ironic and amusing end to the story.
This is so ironic because the paper was so important to Tom at the beginning of the story. It was so important to him because it represented the results of a long period of work for him. It was also important because it would help him get promoted, he felt.
Because it was so important, he risked his life for it and almost died. So it is pretty funny that after he almost dies to get it, it flies out the window and is lost.
This makes sense, though, because it shows that Tom's attitude has matured -- he now knows what is really important.