Eric isn't meant to be the creepy clerk from the beginning
- The credits list Eric's voice actor's role as "Clerk/ Eric", despite not listing other characters with other names they went by. Eric's strange wound is also only called attention to when Monica walks away from "Clerk", and when Rooney can look at the "Clerk" before Monica's interaction with him. Any time the characters interact with "Eric", they never mention or seem concerned about his wound, even the characters who noticed it prior. Considering the game reuses models elsewhere, it's possible that the Clerk and Eric weren't meant to be the same character. In that case, the Clerk could have been just one more of the not-quite-dangerous-yet things Monica runs into (like the old woman in the elevator) before the Scissorwalker appears and things get deadly, and Eric being a Creepy Red Herring was a complete accident.
Leonard's chapter was originally supposed to take place earlier
- Two very strange things stand out about Leonard's chapter. The first is he insists that, despite the Scissorwalker's presence, he has to risk himself to protect his students, shortly before he completely abandons them and goes on a wild goose chase on the off chance that a random island has some answers. The second is that, at the end of the chapter, Leonard returns to Eric and Cobie in a panic with the news that the Oceanus is being targeted and everyone is in danger, as if that wasn't the entire reason he said they were going to the island to begin with. Perhaps in an earlier draft of the story, the Scissorwalker hadn't revealed itself as of Leonard's chapter, and Leonard went to the island for another reason. Once there, he finds the cult and realizes that it was a trap, with the Oceanus being the real target. Then he returns but is unable to warn anyone before the Scissorwalker is summoned. This could also be why Leonard is able to only run into the Scissorwalker in the well in which it was created, because it hadn't been summoned to the Oceanus yet. Even Eric could be partially explained this way, if he wasn't weird yet, but like how Leonard is flayed and Cobie dies, Eric returns from the island with something wrong with him.
Jerome's chapter was planned to explain the explosion on the ship
- One of the most conspicuously unexplained plot threads in the game is the explosion on the ship at the end of Leonard's chapter. While Rooney deals with its aftermath, who caused it and why is never explained and never matters. However, if we presume that Jerome's chapter would have taken place after he holds the Scissorwalker back but before he's accosted by the "masked hoodlums" (who presumably brought up to the island and put him in the coffin), his chapter could have involved his own investigation into what was going on. This could have culminated in him finding out about the bomb, but being kidnapped just before getting to deal with it. Then, the duration of Leonard's chapter would have had the players in the suspense of the Dramatic Irony of knowing that there's a bomb on the ship, and not finding out what happened to it until the very end of Leonard's chapter.
The captain set the bomb to stop Vigo
- Perhaps the biggest question about the explosion is what it was meant to accomplish, as the Oceanus seems crucial to the villains' plans. In fact, in the ending "It's All Too Late", in which the villains win unimpeded, the Oceanus is found completely intact (just abandoned). We know from the end of the game, though, that the captain of the ship was translating Vigo's diary and knew his plan. It's possible, then, that the captain realized he was up against something beyond his means and went full Godzilla Threshold to deal with it: sink the ship and Vigo's plan with it. The captain would have known the ship was carrying the chemical fertilizer Rooney suspected was used in the bomb and been able to jury-rig something. The captain is also a character that, while never seen, is mentioned several times throughout the game. It's possible he was originally intended to appear in an extra chapter and may even be the person in yellow Rooney sees trapped under the rubble the bomb left behind.
