There was no real closure as to the final fate of the Ninja Zords and the Shogun Zords. Where exactly are they?
In A Zeo Beginning, Tommy stated the following: “Now that Ninjor is back at the temple, and the Zords are gone, we’re gonna need help.” This is the only mention ever made as to what happened to the Ninja and Shogun Zords. How exactly they came to be “gone” is a matter of speculation, but presumably it had something to do with Master Vile’s manipulation of time. Whatever the case, the Zords are clearly inaccessible, whether they are operational or not.