Fallout 4 Subdue Graygarden quest is given when you are the over boss of Nuka-world.

You have to take over three settlements.

Does not matter which three. You are given the quest by Shank.

Once done with this quest line things can go back to normal, you may have to do some tinkering with the commands. If you are a die-hard lover of Graygarden this may be a sad video for you. I personally like the robots in the garden, but as you will see at this point in my playthrough I only had two choices.