Its always possible that they are killed somewhere in the story, or just off on another mission.

They've probably got another mission. I bet we'll play Kenshi and Jax torwards the end and we'll catch up with his group at the end.

I doubt they're a team and I doubt Jax and Kenshi are going to be in, tbh.

So what do you think? Johnny and Sonya die?

After Shinnok's defeat, Jax and Kung Lao return from the netherrealm. Kung Lao goes his separate way from the group. It's through Jax's memory of the terrible things he experienced in the Netherrealm that he convinces Johnny and Sonya to go back with him and save the rest of their fallen allies. Raiden, for once learning from his mistakes, insists some team remain on Earthrealm to protect it in there absence. Begrudgingly they train the hell out of the young team, leaving them under Raiden's care and go to the Netherrealm. They get caught there and the young ones go to save them, hence their fight with Sindel and Kitana.

Sounds like a real possibility to me.

I wonder if the conflict in Li Mei's village is what sets the young ones off on their mission. And what did Raiden do with the amulet after imprisoning Shinnok? He seems to know who the talisman is yet why the hell did he give that thing up?

I'm thinking Kotal and Mileena fight over the amulet with Kotal winning, hence taking the throne but Mileena scurries off with the amulet. Perhaps it's in this fight that the adults are either killed or captured. Cassie and Jacqui don't look depressed like they just found out their parents died, they do look worried and unsure of themselves though. So maybe someone in Outworld imprisons them and the kids are off on their adventure.

Not really, at least there's seem to be no indication of that, however, given Cassie's character and personality I would theorise she got involved with Raiden's shenanigans because she's trying to find or save her parents who got kidnapped or something, it's the only valid motivation I can think of. I don't believe she would be leading a team without them otherwise, Cassie, Takeda, Kung Ji and Jaqui seem like an improv team formed out of necessity.

You really think they would send their sons and daughters to hell to save some people they don't even know?

Absolutely not. Cage, Sonya and Jax would go to hell. The idea is to leave Cassie and Jacqui prepared and trained in Earthrealm, IF something were to go wrong at Special Forces.