Game story not progressing

Hello fellow gamers,

I finished the mission search and destroy and talked to Johnny. Went back because I didn’t realize you could save takemura. So went back in a quick save and did that.

I didn’t get a new main story mission so I went out and did a bunch of side quests and stuff like that for 10 hours more of content and started the phantom liberty missions.

Now I realized I might be screwed because I can’t go back to before the search and destroy mission to cause the game to not glitch out.

It’s annoying because I’m 40 hours in and might have to restart my game

I have tried quick traveling and waiting for a phone call and all that stuff.

Anyone have any ideas how to fix it or should I start a new game?