To file your return now, you would need to print it and send it in with a letter attached explaining your situation.

If you previously contacted the IRS and did not have a resolution, contact the IRS for specialized assistance at 1-800-908-4490. 

I would also contact the IRS Taxpayer Advocacy Service. They are a branch of the IRS but they will get much quicker results and deal with the IRS for you. 

You can find out more information and how to contact them here:

https://www.irs.gov/taxpayer-advocate