Okay as the title says Tsuki no Me is very similar to the matrix.Only instead of software we have genjutsu.
So..since the villains are so strong now and it would be lame if they lost, what if they actually succeed and then the story doesn't end.
My theory goes like this:
Madara succeeding in his Plan, but then maybe Sasuke or Naruto managing to break out of the genjutsu (after all once you are struck with genjutsu it doesn't mean you can't break out of it).
Sasuke with his EMS should be capable of doing that maybe.
And remember how the Matrix ended? With a talk no jutsu by Neo.
Of course Sasuke won't do that..but our lovely wannabe-hokage is capable of "talk no jutsu"ing the Juubi itself into destroying the Moon's Eye Plan.
so the analogy is something like
Neo<-->Sasuke and Naruto
Juubi<-->Deus Ex Machina
Just an idea so if you find it hilarious please express it politely