Unfortunately, if you are unable to return to work after 12 weeks of FMLA leave (which would expire November 15th) you are no longer protected by the FMLA provision that requires your employer to return you to the same or a similar position once you return from FMLA leave, so your employer could terminate you if you are unable to return to work for that time.
The only exception to this would be if you qualify as an individual with a disability under the Fair Employment and Housing Act and/or Americans with Disabilities Act.
If you qualify as someone with a disability then your employer would be required to provide you with a reasonable accomodation, as long as you can perform the essential fucntions of your job with an accomodation.
This accomodation can include additional time off that you need due to your disability, so if you are unable to return to work, I suggest that you do request a reasonable accomodation for the additional time off.
If you cannot return to work and are terminated as a result, I would also definitely reccomend that you file a complaint with the Department of Fair Employment and Housing for discrimination in violation of the Fair Employment and Housing Act.
You can do so using the instructions available online here:http://www.dfeh.ca.gov/Complaints_eCompProc.htm
The Department of Fair Employment and Housing will investigate your complaint on your behalf and either file suit on your behalf or issue you a right to sue letter so you can pursue your claim against your employer through a private attorney.
I sincerely wish I had better news to give you, but I hope you appreciate a direct and honest answer to your question.