After speaking with Nadine in the Ark and Dove Cathedral and getting the key to unlock Jackson's sacred praying grounds beneath the wrecked seatub, return to Desmond and tell him the news. Of course, Desmond chastises you for not interrogating the tribal's leader first. Make your way to the wrecked seatub and enter the caverns that hold the leader of the tribals as well as his means of communication with Calvert.
The path to finding Jackson is easy enough; follow the torches to his inner sanctum. Although there are mirelurks in the caves, you can sneak your way through without fighting them. For the more adventurous there are two well stocked and submerged safes, one in the first room to the left of the boat, the other in a long narrow pool to the left of the walkway further into the cave. Beyond this there is a deep pool with an underwater passage to another small room with 20-30 pre-War money scattered about and in a level based locked trunk.
Upon entering the final room, you find Jackson kneeling before a table speaking to what appears to be a holographic talking brain. Let Jackson and the Brain finish, then speak with the Brain. It does not reveal who it might be straight away but explains that it is using the local tribal cult as means to destroy a signal jamming device that Desmond is using to restrict the Brain's broadcasting signal. The Brain is rather disappointed that the tribals take its instructions to mean destroying the mansion itself instead of the jamming device.
Shooting Jackson in the back while he's still conversing with the Brain causes it to react with surprise, then with satisfaction at your to-the-point method of doing things.
In any event, the Brain will tell you to locate Desmond's jamming device, and find a way to destroy it, so the Brain can expand the range of its psychic influence beyond the sea cave. This starts the Thought Control quest. Report back to Desmond in the Calvert Mansion with the information you obtained from Jackson and the Brain while in the cave.