(This is an abridged version of a summary leaving out a lot of the events that lead to it and focusing on the reveal at the end.)
After traveling through the old Hernandez mineshaft with its flesh-covered walls and organisms which served as something halfway between an insect hive and gut bacteria, the group eventually made it to the center and met with the entity at its heart. This presence, when speaking to sentient creatures, takes the form of a villain from their memories. To some, it appears like the eye of Sauron. To Rafe and Rust Bucket, it appeared as Captain Bloth. For the purpose of this summary, I'm going to call this entity Lavos.
After being told that it could reveal "the truth" to the party, and allow them to live their lives "free of this travesty," Lavos finally revealed the horrifying secrets of reality to the party through visions.
They saw endless cycles. The town of Normal would be founded around the mines, spring up, grow, and ultimately be destroyed by the thing below it in a great catastrophe, and then be founded again, time after time in an endless loop. Osiris lab could not stop the destruction from happening, but Lavos could not truly break out of its containment either.
In every iteration, Rafael Hernández would be there at the founding of the labs, serving as a board member, until his son, Javier Hernández took over. Javier would adopt a young boy, Rafe. And Rafe would be there in the next iteration, growing older and founding the labs again and serving as a board member until his son, Javier took over, adopting Rafe to start the cycle again. Javier was alwas slightly different in each iteration, having different biological mothers, but every Rafe was identical. In every iteration, Rafe also had some version of a robotic companion along with him.
Beyond that, Lavos revealed the existentially terrifying knowledge that none of what the characters knew was truly real. Jack Carter, for example, saw visions of himself in another dimension through the lens of a television show.
However, it offered them all a way out. If they could bring it Rafe, it could help them escape the loop. They would be able to escape into a perfect reality for them where they could live the rest of their existence as real entities, alongside those they care about. And with the loop broken, it would be free to do what it wanted with the world they left behind.
Lavos was able to teleport the party members who were physically there away, with its last instruction to bring it what it needed. Meanwhile Abigail, still physically stuck at the lab, spoke with board members of Osiris labs, and argued that she could help them to stop the creature if she were released.
The whole group faced a difficult decision that would guide the rest of their journey. Should they help Lavos to bring about an end of the loops? Should they help Osiris labs to contain it and perhaps come up with a more permanent solution? Or should they go their own way and try to discover an unknown solution, working with neither of these two powerful but dark entities?