Here There Be Monsters

If you head east of Harbormaster Hotel or SE of Shamrock Taphouse, you'll come across a kid named Donny in an old boat house. If you talk to him, you'll get this quest. In the other hand, you can also start this quest by swimming to the marked location.

Approach Captain Zao and talk to him. If you agreed to help him, he'll send you to get some dampening coils from Saugus Ironworks. The dampening coil is found in Saugus Ironworks' Blast Furnace, the same room where you'll have to rescue Jake Finch in the quest "Out of Fire". Next, you have to get the warhead from below the submarine. The inner chambers of the sub has feral ghouls, remainders of the crew. The path is pretty much straightforward so you'll reach it without too much navigation. Once you have it, deliver it to Cap. Zao again.

Now you have to head back to the reactor and insert the dampening coil first before putting in the reactor. Once done, talk to Zao again to receive your payment including three Homing Beacons to call in a tactical nuclear strike. Unlike the Minutemen's artillery support, this is the only set you'll get for the entire game so save them or use them wisely.