So, started a new play-through after not touching XPiratez for a while, on John Silver. Early April of the first year, and the Ninjas drop some massive HQ right next to my base; my airbus can't leave the base without getting swarmed and shot down. Restored to a previous month and continued from there; the Ninja base still spawns and seems to be in a slightly different place but still close enough so I can't launch aerial interceptions. I can attack the base with my V8; but in that case it's 5 of my soldiers vs dozens or hundreds of enemies, and I don't have the equipment to even begin to deal with this.
Is this really the intended behavior?
I see four ways forward from here: limp along using only the V8 to perform missions while building a base somewhere else that I can use as my intercept base and hope I don't run out of money & score while that happens, call this run a wash and start a new play-through from scratch, edit my save game to move the ninja base somewhere further away, or attack the base and use debug mode to "win" the mission while making exceptionally rude hand gestures.