Before beginning this step, make sure your guns are Pack a Punched and that you're ready for a big fight.
Give the Seal to the Hermit. This will trigger a lengthy lockdown sequence in the lighthouse.
After finishing the lockdown, take the seal back from the Hermit and follow the Lighthouse beam to PaP machines. Place the Seal into the machine and fill it with Zombie souls. Repeat this process for every PaP machine. The order is typically Beach---->Lagoon----> Sunken Path----->Boathouse
After placing the Seal in these 4 PaP Machines, return the Seal to the Blood. Repeat the step of shooting the Blood and freezing the orange orbs, then place the Seal onto the campfire and throw Sam's music box at it.
After the dialogue finishes, collect the Seal and head to the Golden PaP flinger on the Sun Deck.
Place the Seal into the Golden PaP. This will trigger the boss fight.
There is a radius of safety near the Agarthan Device. You will take damage if you go anywhere else. Stick close to the Agarthan Device. If you lose track of it, you can see it through walls with a green outline. The Device will sometimes stop, which means that there will be a brief soul collecting phase, after which there will be a carpenter and max ammo. Keep an eye out for lava sections, where you will have to do a few jumps on stones to avoid lava damage.
The Agarthan Device begins in the Forecastle, it quickly travels to the Main Deck, where there is a lockdown event. The Device will take the stairs down from the main deck into the Cargo Hold, and then into the Artifact Storage. The first lava section is in Artifact Storage.
The Device then travels through the Sunken Path, to the Lagoon, and then has a lockdown event at the Lighthouse Cove. From the Cove, it takes the Hidden Path, with a brief lava section. It drops onto the Beach, through the Lighthouse approach, and has a lockdown event in the Lighthouse Station.
The Device then travels up the lighthouse and takes the zipline to the Facility. Importantly, wait as long as possible before taking the Zipline, so you don't take too much damage from getting to the Facility too early. The Device goes through Decontamination, down into Human Infusion, where it stops for the last time. This final lockdown sequence is not about kills, but about time. You must survive for roughly 1 minute 15 seconds, as the radius of the Device's protection gets smaller and smaller. A special weapon is highly recommended for the ending, when the radius is tiny and nearly impossible to survive without.
After completing this lockdown, you will receive one final bit of dialogue. Take the Device, and give it to the Hermit. Travel to the Sun Deck, and the Hermit will fulfill his destiny. The Device will drop to the Forecastle. Take the Device and the cutscene will play.