Please review what your offer letter says. Usually, every offer letter contains a clause stating that if an employee (e.g., XYZ) is absent from duty for a consecutive number of days (x days) without providing any information, it will be treated as termination, etc.
If this clause is present, you should consider treating him as a new appointment if a suitable position is available within your organization. Of course, conduct a thorough background check. Ask him to provide all the relevant documents, including doctor's notes, to address your concerns. It is surprising that he did not inform you about his absence for three months in today's world. Personally, I cannot justify this.
Thanks,
Manish