I have fell at work in July,I am collecting workmans comp,I fell behind in rent two months,he is sueing me for back rent,the apartment I am renting is illegal,the landlord has no permit,what are my rights

The Court will not award him back rent if the apartment is illegal. The Court will also order you to get out and tell him to shut down the apartment until he gets a permit.

The only time I've seen this any different is when the tenant KNEW the apartment was illegal, moved in and agreed to pay rent and then argued the illegal apartment as a defense.

Court decided tenant couldn't have it both ways.

Yes you will be evicted a lot faster for an illegal apartment than for merely not paying rent.

So try and work out a payment plan

It appears you had no problem renting an illegal apartment, and no problem paying rent for a illegal apartment, and now that you can't pay ( guess you expect them to let you live free?) they are not a illegal charity either.

You agreed to pay, will get kicked out either way, one just hurts the other person also.