Exactly, the show is a show, those comics were a cool idea for hardcore people who wanted more.
But the true story is the show, the 4 seasons plus this new 5th season.
Maybe in 2017 we can get a cool Blu Ray box set of ALL 5 seasons?
Godzilla | Star Wars | Marvel

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Tartakovsky didn't work on those comic books and earlier this year he said that this ending is non-canon. We'll see the real ending planned by Tartakovsky in the final season of the series.

I remember reading that even when the show originally got cancelled, Tartakovsky continued it in comic book form where it did finally have a proper ending. I've seen some people complain about the ending, but it makes perfect sense and was even hinted at in one animated episode.

The New Number 2: "Are you going to run?"
Number 6: "Like blazes. First chance I get."