All of the stories including MK9 end up like this though. Half the cast was murked by Sindel in MK9. Then Raiden accidentally killed Liu Kang. The last few chapters of MK9 was Raiden making mistake after mistake. MKX saw some revenants like Jax and Sub Zero restored (even if it skipped over the fact that he was Cyber Sub Zero and wasn't supposed to have a soul when he was "killed" in MK9). Shinnok, an elder god, was defeated twice (once by Johnny and then by his daughter). MKX also made jobbers out of most of the cast. Cool story that set up what looked like a dope rivalry between Dark Raiden and Liu Kang and Kitana. MK11 undid it all by introducing Kronika. Aftermath gave us a better story.
Overall, this is my ranking of the story modes:
MK1
MK9- this would be #1 if we didn't lose a lot of the roster to Sindel
Aftermath
MKX
MK11