I really like your article, the formatting change makes sense, much like the owl, and it is an interesting way to present it. I won't go through the entire piece like I would with others, and just focus on minor points
Why do you dare try to document the forces you do not comprehend.
This should have a question mark, not a period, or change it to be more of a statement
No person who has ever been trapped in this hell with me has escaped
The only vice I must live with is the curse placed upon me by my creator.
I don't think vice fits that well with the sentence. Vice is a thing you enjoy doing that you shouldn't do, and can become addicted to doing, but it doesn't sound like he enjoys answering questions.
I only ask that you please do your best to entertain me before you expire.
The tone of this sentence is very different from the rest of the article, because the anomaly is normally very condescending and high and mighty, whereas this makes it seem more polite and considerate.
No, I'm sorry to say but we won't honor you with your wish
This feels like a weird way to word this, I feel like an easier way would be to say, "We cannot honor your wish"
Alright all done with Part 1 of d4rkseid's bizarre adventure, "Phantom Thought,"
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Moving on to part 2, "Mental Tendency," has a few issues, but they're mostly continuity errors
Only you know they won't be walking out with a plus one that night.
This sentence is structured very weirdly, and I can only tell what you're saying based on other statments.
You were fine with not knowing why these things are done.
Do you mean to say that "You" are not fine knowing why things are done? Otherwise it goes against the rest of the paragraph.
They never cared for me. They never cared for anyone, but you knew that.
I can't really tell what's going on in this. Are the 1st sentence, and the 1st half of the 2nd sentence an inner thought? I also think the "but" should be turned into an "and."
I'm not going to quote the final paragraph, but throughout the 1st and 2nd pages the article implies that the researcher knows that he will be stuck with SCP-004 for all of eternity, but this final part states that they didn't know the entity would be conversing with them. Other than that, I like the final poem.
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On to Stardust Vocal-Cord-Cutters
You feel the warmth of the blankets compressing your body into the hard bed
I understand that you don't want the researchers return to consciousness to be a positive thing, but that's a bit too cruel to the blankets
you'll be alone with your thoughts again… and that thing.
No other problems w/ part 3