If you were legally married on or before Dec 31 of the tax year, then your only filing status options are Married Filing Separate, or Married Filing Joint. Period. For a married couple to file separate is almost always the worst and most $COSTLY& way to file tax-wise. When a married couple files separate, they both *automatically* disqualify themselves for tax deductions and credits they would get if they filed joint. So you should file a joint return.
For the CA state tax return, it is *IMPORTANT* that you and your spouse BOTH read https://www.caltax.com/wp-content/uploads/2018/03/NonresidentsONLINE.pdf starting on page 50, "California Military Personnel assigned to stations outside California". Additionally, the active duty military member should read https://www.dcms.uscg.mil/Portals/10/CG-1/PPC/guides/gp/spo/Deductions/State_Tax_Withholding_Excepti... for what to do via their CAC login to stop CA tax withholding, if they qualify.
