Thanks to an update to the law, military spouses can now choose to file state tax returns in their active duty servicemember's home state, whether they have ever lived there or not. So you and your spouse can file a joint return in the state that is your home of record.
Alternatively, your spouse can choose to file in the state in which he or she has established their own domicile. The choice is theirs.
https://www.military.com/money/military-spouses-residency-relief-act-mssra