Not unless you count a Japanese tax return as being the other tax return (and I don't honestly know enough about the Japanese tax system to tell you about that, without doing further research). For for US tax purposes, though, if you went with filing Option # 2 (a joint tax return, including your spouse's Japanese-source income) then that means only filing one return; and if you went with Option # 1 as suggested (filing a Married Filing Separately return for just yourself), then your spouse doesn't need to file a comparable MFS tax return . . . because for the 2016 tax year she was a nonresident alien with no US-source income. So, either way you look at it, no, you really don't have to file two returns for US tax compliance purposes. Thanks.
