Firstly, Meta Knight shares several similar physical traits to Nightmare. His shoulder plates are almost identical to Nightmare's in design, although this could be discounted, as these have been a part of both their designs since their early appearances in the video games. However, Meta Knight also folds his cape around him in the exact same manner as Nightmare does. This did not occur until the anime was released. His eyes also change color, which appears to be an unusual trait for a Star Warrior (like Chilidog/Wolfwrath's gem, but this is almost certainly a coincidence). If the games and pilot anime could be taken as a reference, he also has demon-like wings.
Meta Knight also tends to have a rather stoic personality. This may be due to mental scars from the war, or even simply just a personality trait, but he also seems to be sporadically angry on occasion, especially earlier in the series. And like Nightmare, he also tends to stay on the sidelines, rarely interfering unless he believes there is truly danger.
He has an uncanny ability to know the names and abilities of nearly every demon beast, although this could, again, be blamed on the war.
Meta Knight doesn't appear to hate demon beasts, either, for example allowing Lololo and Lalala to carry him - but on the other hand, he loathes Nightmare.
Oh, and did we mention Lololo and Lalala happen to be failed demon beasts?
Another thing worthy of note is the scene in Episode 3 when Nightmare is depicted as creating and placing a round, blue piece on the chessboard - which happens to use a sword to represent its rebellion against him.
There are two main pieces of evidence supporting the theory. One is the following dialogue from Episode 3, beginning after Kabu tells the story of Nightmare's failed creation:
Fumu: That was a Star Warrior?
Bun: So that's why Nightmare wants to get rid of (Kirby)...
Kabu: I do not know if it was Kirby.
Bun: But Kabu, how do you know about these things?
Kabu: I heard it a long time ago from Sir Meta Knight.
And at the episode's conclusion:
Fumu: Is Kirby Nightmare's failed creation? Don't you know everything?
Meta Knight: ...How would I know of that?
As well, Meta Knight knows exactly where the delivery system is in Nightmare's headquarters. This is a near-dead giveaway, as no Star Warrior or GSA member had ever gotten so far into Nightmare's base prior to the infiltration in episodes 99 and 100, and none of the others in the party were aware of its location.
Coincidence? We think not.
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