- After Elro killed Grey, by all rights he should be a wanted criminal. He should have gone off the grid entirely trying to get away from One Concern and Agent Black. Instead, he continues to live in Settlement 17 with his wife and daughter, and still goes to work at the same job where he murdered a high-ranking agent.
- To be slightly fair, Elro is almost certainly lying to his family about going to work, but it's still odd that he puts his family into that much danger. As shown with Mr. Andress, the husbands, wives, and children of sinners are not punished for a family member's sin. Elro was friends with an agent and knows a lot about the Concern; he should know better than to go back home and recruit his sister to do private practice in his house while wanted by the people currently occupying Settlement 17.
- Judging from Elro's discussion with his wife, he's been on the lam this entire time, and that he's been lying to everyone about his situation. He pops into his home to give the appearance that everything's okay. Given that the Concern wants to give the appearance that their Agents are invincible, putting him on a Wanted List for "murdering an Agent" would likely be demoralizing to those in City One and the believers of the Concern. So they swept it under the rug and gave the Agents the order to kill him, but with due discretion. After all, he has the means to kill them, and it would be terrible if the Isi caught wind of his methods. That said...given the writing, it's equally possible that Konjak didn't think of Elro's assassination of Gray until late in development, by which point it was too late to redo earlier scenes to reflect that.
- Just what was the "big secret" that Agent Black hinted at before the Agent White fight? Was it that there was another ark ship at City One? Because that doesn't make sense, if only due to the fact everyone in the game is at least somewhat aware that they're colonists from another world.
- What even is this story? How does GENERAL Chrome not know about the giant tower his military is running, but Black does? Why does the tower even exist? Why does Royal get no response from betraying his own side and actively fighting against One Concern? What do people know about the Starworm? There are pictures of it hanging around. Was it just chilling out for centuries next to the moon before deciding to check the planet out and/or refuel? Why does the religion require ivory and disallow research into other energy sources, but the Starworm (who is worshiped and presumably started their religion) not want them to use ivory? What are the blue eyes? Are they supposed to be on the Starworm? Then why do they look like parasitic tumors? Why was this artificial planet built in the first place? If it's just a tanker, why make trees and oceans? The moons both hold ivory too, so are they also tankers? Just without trees? How is everyone immediately alerted the world is ending? Do they see the Starworm coming? Then how is there still the hours necessary to activate a rocket and travel to the moon to visit it? What does the average person even know about their own world or religion? Apparently continents move around regularly so there's no way to make a complete world map, but One Concern is trying to hide this fact? Why? It's hard to not notice there was one writer and no editor.
Headscratchers / Iconoclasts