I feel like this article would be substantially better if it were pared down - less ambitious, less audacious. Not every article has to introduce a major new thing to the universe, or be a Grand Unified Theory behind a whole bunch of SCPs. IMO it would be better just being a small interesting thing that haunted a group of researchers for a while. No need to create an O6 council (that annoyed me), no need to have Mary Nakayama, no need for the clear comparison between 4023 and the Factory. Plus some of the symptoms caused by the anomalous objects were… just too much.
Just too much melodrama. It needs to be smaller and more self-contained, and not lean on every other part of the universe so much while attempting to change them and multiplying entities.
(Like other readers said, there are also quite a lot of obvious grammar errors.)