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Ninja is a boss battle in SaGa II/Final Fantasy Legend II and a fairly significant villain, he (alongside many other monsters) raiding the Guardians Base and stole all the magi they had collected from across the world on behalf of "new gods" - Ninja kidnapped Lynn in order to lure the main protagonist's father out, who was acting as her guardian at the time (and was also a major figure in the Guardians): Ninja threatened to kill Lynn, prompting the main protagonist's father to leap at him into a portal - the heroes think that this marked the end of both but a short while later the lone Ninja appears, taunting the heroes before engaging in a fight and is defeated.
For a fairly long period of time after this event the heroes were left thinking that Dad (he had no real name) was dead, however this was not the case - as for Ninja, it seems likely he was slain after or during the battle with the heroes.