Yes, you can file jointly. Where you file depends on the residency status for you and your spouse as well as who has the highest adjusted gross income. Here is the Publication 570 reference; check the general rules for military and the special rules for Guam.
As a an active duty military member you do not lose or gain residence that is due to a military move. So, for example, if you were a bona fide resident of Guam before joining the military then you still are and you and your spouse would file a joint return with Guam with all income. No US or state returns would be filed.
If you were a US citizen before joining the military then the state you joined the military from is your home of record and resident state. In this case you could file a joint return based on who has the higher adjusted gross income (AGI), you or your spouse. If she does, you file a joint return in Guam and include all income; there will not be US or state return filed.
If you have the higher AGI, you'll file a joint US return and report all income and Guam return will be filed.
If you are a US citizen with a resident state and you file a joint US federal return. You may be able to file a separate state return with only your income/deductions; it depends on the laws of that state.
Finally, if you are not a bona fide resident of Guam, but have a resident state, you may choose to file separately. You would file a US and state return for your home of record state as Married Filing Separately (MFS). You spouse, since you lived apart and she provided a home for dependents could file as head of household (HOH) in Guam with only her income/deductions.
Unless CA is your home of record or you had CA source income other than your military pay you do not have a filing requirement in CA.
To help you calculate which filing has the best overall tax results for you, I recommend using a TurboTax desktop product. There in one product you can create the various filing scenarios and use the one that is best for you (Jointly or MFS/HOH).
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