The second movie was based entirely on the game - same story, same costumes, almost all the same. The first was just an adaptation - and was better, a lot. Ironical.
The story wasn't even based entirely on the game though, pretty much none of it actually.
In comparing the roles of all the characters plus the flow of Annihilation story, it was a complete departure from what made MK3 good, characters like Mileena, Sektor, Nightwolf, Sheeva and Sub-Zero became filler characters.
The story was very bare bones, touching on none of the good stuff from the games to be honest.
Kitana wasn't a damsel in distress waiting for Liu Kang to save her, she escaped on her own and was hunted by Reptile and Jade.
The problem with Annihilation is that they compacted a bunch of fights together without substantive depth or story elaboration.
The firsr movie had less fights, but focused on the mythlogy and story, which is why it was good. They referenced almost all the game stuff, but added onto it with things like Liu Kang having a brother..but it was generally true enough to the game.
These are just a couple things, but there's a huge list of why MK Annihilation wasn't good it never really stood by what made the Trilogy great.
The costumes were the only thing closer to true to the games.
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