It would seem that Injustice 3 follows up where Injustice 2 left off. Unlike the games, the comics provide much more explanation of the Injustice universe. A great deal has been put into the games from the comics. While the game Injustice 2 left players to make their own choices, the comics made one canon.
In no way do I intend to imply that particular comic book choices will remain canon. There is every possibility NetherRealm Studios will decide to take an alternate approach to the story. It's hard to pick between the two endings since both are quite intriguing, but since there's a new He-Man movie on the way, NetherRealm may want a different approach to the series.
Injustice 3 Rumours: Release Date, Platforms, Roster, and More
Injustice 3 Might Have He-Man and The Masters of The Universe
I won't give you any spoilers about the "Injustice Vs the Master of the Universe" comics since I don't have to, and I think you should read it for yourself. My focus will instead be on Injustice 3's beginning since that is the most crucial aspect.
A choice had to be made in Injustice 2 with either Superman or Batman winning. If Batman won, Superman would go to the Phantom Zone, and if Superman won, Batman would supposedly be put under mind control and become the Black Oracle. This image appears in the Injustice Vs. The Masters of the Universe comics:
So that means Superman won. Then, He-Man and his compatriots then join the fray, and more happens. So either Injustice 3 must follow the story of Injustice Vs. The Masters of the Universe, or it must be set after the comic, right? Not at all.
It's excellent news that Kevin Smith (the guy who made Clerks) will direct a new He-Man movie so that the character will be in pop culture just in time for Injustice 3. To market their film further, Mattel might let NetherRealm create a version of Injustice Vs. the Masters of the Universe of their own. It's a good idea if you can both market your movie and make money simultaneously.
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It is possible for NetherRealm to disregard the endings altogether. A specific event may have occurred just when the decision needed to be made. In NetherRealm's case, it makes sense.
It is important to keep in mind that Injustice 2 was released in 2017, and the comic continuation was released in 2018. Injustice 2 did not know where the story would go in the future and may not have known it would get a crossover or that He-Man would be turned into a movie years later.
There's a lot to keep in mind, but what's important to note is that He-Man will most likely play a part in Injustice 3.