I'd highly doubt that it was a vessel or a sea installation as the JSDF would've been able to easily pinpoint the area from where the missiles were fired (especially as we're talking of a missile fired ON A PLANE RIGHT ABOVE TOKYO... although why they just didn't blow up the plane in two was a good question *nvm... I think I know why*).
Unless EU itself has infiltrated the JSDF... which would be... well, would make more sense. :P
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