I thought the ghosts were the strongest part because it showed the story had the confidence to continue introducing new crazier ideas, and that one was particularly crazy but still fit into the SCP world. Sort of like why people liked Three Body Problem.
The weakest parts are when it focuses too much on the antagonist, where it tends to forget the actual definition of 3125 and just makes it something/someone that causes the world to end in random wacky crazy ways.
When it gets post-apocalyptic the writing also tends to forget how travel times and geography work. (Pretty common problem with old SF, where you'd go to a "planet" and there are like, 3 people who live on the planet. In this case the remaining living protagonist somehow manages to walk between very far places on his own without needing food and such.)