The closest I found to a workaround for this issue was to reload an old save, from before I had manually attacked the Prydwen. After doing that, I found the Underground Undercover quest progressed correctly with the following in-game state:
- Glory is alive.
- BoS members on the airship are alive.
- BoS members on the ground at the airport are alive.
- Paladin Danse is dead.
- The 'Underground Undercover' quest wants me to warn Desdemona.
- I haven't progressed the 'End of the Line' quest past the point where it wants me to talk to Father.
After that my game worked as it should (got to fight off the BoS attack, got the mission to attack the Prydwen, looted Final Judgement off of Maxson's corpse, was able to warn Desdemona again after talking to Father, etc.).
Another interesting thing I found was that if you progress Underground Undercover to the point where it wants you to clear the control room, you can instead turn around and take the elevator back into the Institute proper and pick a fight with everyone without getting banished. Among other things, that lets you take out members of the directorate and other named Institute NPC's who disappear if you just keep progressing Underground Undercover.
If your current quest objective is to follow dogmeat, and you have the quest marked in your Pip-Boy, then you should have a quest marker leading to him. If that objective is complete, then you simply need to enter Kellog's base to continue. If it's not complete, but there's no marker, here are some things you can try:
Finding Dogmeat
I don't recall any law enforcement robots on the trail, but there is an assaultron shortly after passing Forest Grove Marsh. There is a cigar on the box the assaultron's wreck is lying upon, which is the clue here. You're supposed to grab it and show it to Dogmeat. If you did this, then he would have started toward the next clue. It doesn't seem like you always need to actually kneel down and show him the clue. Sometimes he just takes off.
If this is where you are, then the next clue is a bloody rag on a chain link fence up the hill toward the Greater Mass Blood Clinic. After the robot, continue up the road a ways until you get to the intersection. Take a right, then veer left up the hill.
The rag is next to a break in the fence that you can walk through. Maybe Dogmeat is over there. That's the last clue before Kellog's base
at Fort Hagen.
Entering the Base
If you can't find Dogmeat, that might be okay. I've previously ditched Dogmeat and ran ahead to enter the base, and everything went fine. I can't recall if that was definitely before the last bloody rag, though.
To do this, you need to enter
Fort Hagen, and get to the basement via the elevator after the ceiling turret. This elevator will be inaccessible before a quest trigger in Reunions, so if it doesn't work when you get there then you've missed a quest trigger and have a problem.
To get inside, you can either take the roof entrance or go in through the basement.
The roof entrance of Fort Hagen is guarded by a bunch of turrets. You can completely ignore and avoid these by using the door in the Parking Garage next door. Go down the stairs. You'll find a hideout room with a dead person and some supplies. Leave the room toward the main part of the garage, and you should find a blue door on the same floor.
Go in, and it should complete the "Follow Dogmeat" objective.
Load and Try Again
If you find that none of this works, then you'll likely need to load a save from before the robot.
If you're playing a Bethesda game and you don't have a trail of saves to go back to, then you're doing it wrong. Anytime you do something you don't want to do again, save.
Best Answer
The faction quests during this part of Fallout 4 are heavily intertwined, and prone to bugs if you try to do too many things at once. It sounds like you've got yourself in a situation where Ayo is locked up in too many things and can't do any of them.
Mankind Redefined probably got screwed up when you started Mass Fusion after Tactical Thinking. If you can go to a save before finishing Tactical Thinking, that might fix it.
Otherwise, it sounds like you'll have to continue the game with the Brotherhood. You would be unable to do any further Institute quests after completing Spoils of War anyway.
If you were on PC, I expect you could use console commands to finish Mankind Redefined and continue, but you've indicated that you're playing on PS4.