.. What do I do with Alec's letter?

After you talk to Alec after your room gets trashed --

My room has been ransacked!

-- he'll blurt out some information, then hand you a note and a letter and disappear. You won't see him again, though you'll hear from him later.

The note (on white paper) tells you that the cards he took from your room are in locker 36; go get them.

The letter (on yellow paper) gives you all kinds of information about him. It seems pretty clear now that Alec was not your enemy, though he was helping Revenant, however unwillingly.

As a side note, remember the person who told you Alec was a liar? That person should now be a definite suspect in your eyes.