If your statement is correct, your client could be in breach of immigration regulations but that does not negate his/her filing requirements.  You would prepare the return based on whether he/she was a resident alien by Substantial Presence Test, taking into account various elections and exceptions available under §7701 as well as treaty articles, where applicable.

A non-citizen who is not a green card holder with only an ITIN is not authorized to work in the US (unless he/she was in the US only on business trips and the activities were within the limits of a B1/B2 visa).  So, there may be more to worry about than tax and, if true, he/she should be advised to consult an immigration attorney.