http://db.gamefaqs.com/console/gamecube/file/mortal_kombat_history.txt

This has all the bios and endings from every game.

MKT overrides the MK3 and UMK3 endings/stories. Everything in MKT is what actually happens (for the most part)

Mortal Kombat Trilogy is yet another upgrade version for MK3/UMK3. One reason that I heard why MK Trilogy was being made is because of Sega Saturn buying the rights to have the only "arcade replica" of UMK3. Not the SNES, or Genesis knockoffs of UMK3. So for the other systmes to get any version of UMK3 they had to change the name, and since doing so, they added more features but then they added the game to Saturn as well towards the end of Saturn's product line here in the US. It was in an EGM2 magazine article with the first shots of MKT. Some of the first shots show Human Smoke doing Scorpion's Hellraiser Fatality which was later changed of course. Anyway, MK Trilogy ends the saga behind Shao Kahn's takeover of Earth, and begins Shinnok's new invasion, and tournament in MK4. Read Noob Saibot's ending, it depicts Shinnok in a way.

As others have said, it is actually what happened during Shao Kahn's invasion. It doesn't fit with MK3 or UMK3, it overrides them. Think of it like a movie getting an extended edition. It's the same story, there is just more told.


As for differences...MKT added characters like Cage, Raiden and Baraka so obviously their stories are new. It also changed a few endings, like Ermac and Mileena, to make them more interesting and to set up future games.


A few things are non canon or just there to be a compilation. Goro and Kintaro are the big examples. Neither have stories or endings. They are just there as a bonus.