Hi,

My girlfriends lease to her apartment just ended on March 31st but she has been staying with me in my apartment before the 31st to the present day. I also had to leave town for a few days in March and I let her borrow the key to my apartment so she could sleep in my room. On the 31st of March she moved all of her stuff into my room. My roommate then sent me an email stating that she is living in the apartment which breaks the Number of Occupants rule on the Lease.

The lease states: The Lesse shall not assign nor sublet any part of the whole leased premises, nor shall permit the leased premises to be occupied for a period longer than a temporary visit by anyone except the individual specifically named in the first paragraph of this lease, without first obtaining on each occasion the assent in writing of the Lessor.

What should I do? Do I have to make her move out? Can I ask the landlord to let her stay? She signed the lease to legally move in on September 1st 2007.

Sounds like your roommate doesn't want her there, and lease has this covered. You either need to make a good faith effort to make his acceptable to both your roommate and your landlord (money usually helps, but don't ignore making sure she is not a burden) or find her another place. Trying to find a loophole will only create bigger problems if she's not wanted!
BTW, you would have been much better off to have discussed this with your roommate BEFORE she moved herself in!