This isn't really freeware per se... but you can just get trial versions for Microsoft OneNote and/or Agilix GoBinder. Good for at least 30 days, you should be able to do your assignment before they expire.
Print the PDF file to Microsoft OneNote and you can then write on it there. You can use either 2003 or 2007, either will suffice.
Another alternative is Agilix GoBinder. I wouldn't buy it now that it seems to have fallen out of support, but again, download a trial version. Print to GoBinder and you can annotate there.
Alternatively, if you can get a hold of a Tablet PC with either Windows XP Tablet PC Edition or Windows Vista, you can just use the bundled Microsoft Journal program as well (again print to Journal).
For all three of these solutions, you will have to install the corresponding print driver for the software. But I know for a fact that all of them have print drivers that allow you to print to them as if they were a physical printer. (I've used all three of these programs before personally)
Edit: If you absolutely must have an end product of 25 pages, then I suggest to jump straight to either Agilix GoBinder or Microsoft Journal. Microsoft OneNote's pagination is a bit difficult to predict. Journal works the best. But GoBinder is very workable.