Cliché Storm: Many of the tropes found in video game creepypastas are found here played completely (and unashamedly) straight. Particularly egregious examples include the author's obsession with listing the exact amount of time things happened for, constantly jamming things from other games into the story simply because it might be "scary", and of course, hyperrealistic blood.
Common Knowledge: X is often interpreted as a demon, when he's actually an alien. Him being an alien was made more clear by JoeDoughBoi and ASTRANOMICONX, Sonic.exe's new owners. Then again, various aspects of the original story and its sequel don't exactly do anything to avoid creating the confusion in the first place.
X is a monster resembling Sonic the Hedgehog. Trapped in another dimension, X created a cursed Sonic game. Once someone had played through the game, a portal would open up, allowing X to tear the player's soul out of their body and take them back to his world for eternal torture. When Tom plays the game, he witnesses X torment several people whose souls have been transformed into Sonic characters, before he brings Tom into his realm. In Sonic.exe Round 2, it is revealed that X has killed 31 people, and plans to one day permanently cross over to Earth and turn it into a realm of eternal suffering. Viewing all of humanity as toys for his amusement, X is as evil as a Creepypasta monster could be.
Condemned by History: You would have nary a clue this used to be one of the most well-respected game Creepypastas out there judging by how the pasta is treated nowadays; after critics tore it apart and made people realize its flaws, the pasta was lampooned so hard it got moved off the Creepypasta Wiki and onto a wiki dedicated explicitly for bad or troll Creepypastas. This in turn led the author to practically explode with petulant rage, writing a response to the Creepypasta Wiki's deletion of the story (with an archive available HERE) so overwrought and laden with Purple Prose that he only drew further attention to both the story and himself, resulting in even more relentless mockery and criticism. Finally, it was revealed in 2021 that the creepypasta author participated in questionable roleplays with minors, leading to said author being disowned by most of the fandom. While there does still exist a significant following for the general idea and character of Sonic.exe (ironically, something the author's response outright desired to keep alive), especially among kids or adults who encountered it as kids, it is almost entirely divorced from the actual original story, which any retrospective will be quick to point out the issues with.
One exists with Super Mario Bros. Z due to the latter's Big Bad, Turbo Mecha Sonic, also having an A God Am I mentality, so they have Mecha and Sonic.exe duke it out to see which of them deserves the God title. Though this rivalry is heavily onesided; most who know about it take Mecha's side and have him utterly trash Sonic.exe, even if the latter fights back (it helps that Mecha is considered more terrifying than Sonic.exe). Even when Sonic.exe was Rescued from the Scrappy Heap by the Friday Night Funkin' fanbase through the Vs Sonic.exe mod, it amounted to nothing, because kkirby999, a fan of Super Mario Bros. Z, made a mod where Boyfriend faces Mecha, which led to other SMBZ fans to make covers where Mecha trashes the characters in the Vs. Sonic.exe mod.
Another animosity of an even bigger magnitude exists with Mega Man Battle Network. Case in point, that series has a lot of .EXE characters, but none of them are demonic soul-snatches (the closest instance is how MegaMan is Lan's brother Hub having undergone Brain Uploading, and that still doesn't count) and many of them are actually benevolent and friendly. And then, as the Battle Network fans would claim, Sonic.EXE came around and posed as a NetNavi to ruin the good name of the true NetNavis. Needless to say, the Battle Network fans will rise with pitchforks against anyone who likes Sonic.EXE.
First Installment Wins: While "wins" is a bit too much of a term, the original pasta is given a small credit due to having a more straightforward plot that does not drag out for too long and featuring little if any Purple Prose, something both the sequel and the remake suffer from greatly.
There would eventually be an official Sonic media with a human protagonist named Tom. Funnily enough, it also had a version of Sonic that made people reel in horror. That very same version of Sonic (albeit with a few cosmetic changes) was later featured in Chip 'n Dale: Rescue Rangers (2022), where he does a creepy closeup at one point similar to one of Sonic.exe's faces.
In his infamous rant, the author claims that "our glorious little Hellspawn shall have the last laugh yet" and tells his fans to do whatever it takes to keep it alive. By 2023, Sonic.exe has, even if they're rather divorced from the original, maintained a strong community of fan-games, fan-videos, art, and mods compared to other creepypastas, even fellow big-namers like Jeff the Killer and Slender Man. So, in a sense, Sonic.exe did get the last laugh.
I Am Not Shazam: "Sonic.exe Round 2" reveals the antagonist's name is "X". Virtually everyone on the internet calls him "Sonic.exe" (despite that being the name of the cursed game).
It's Popular, Now It Sucks!: Ever since it was posted on the Creepypasta Wiki and the fangame adaptation, it has gained widespread popularity across the net, and since then many find it as one of the worst examples of creepypastas out there. This trope, among otherreasons, is the reason it was moved from the Creepypasta Wiki to its sister site, the Trollpasta Wiki (along with many other old creepypastas that fell into this trope). Even amongst its initial following, it didn't really stand the test of time against other pastas.
Sonic.EXE's backstory. Specifically, the fact that he became a fan of the series and goes after people that hate the Sonic games kills any dramatic tension that the original story had.
The Gods in the Cult of X in Chapter 2, who show up, are introduced as "[Insert Emotion in Japanese], the God of [Insert Same Emotion in English]" and then promptly vanish from the plot.
Nightmare Retardant: Pretty much the entire thing could count, but here are some highlights.
The story also has a love for repeatedly listing or estimating an exact number of seconds something happened. This can get pretty tiring. This culminates in a moment near the finale, in which our protagonist 'in an actual split second' screams - must have been a very short scream! - then yells for 7 seconds while the game produces static for the exact same amount of time, cramming in a healthy dose of Purple Prose for good measure.
Suddenly in an actual split second I screamed as Sonic lunged at the screen screeching loudly with his mouth wide open to an unnatural length revealing nothing but a literally spiraling [sic] abyss of pure darkness before the red static came again, this time much louder and distorted, so loud that it hurt my ears, I yelled and grabbed my ears as the red static screeched for a good 7 seconds.
The excessive use of red and black throughout the story, as if they're the only evil colors in the color spectrum.
The constant ripoffs from other video games (ripping off the final boss music from Silent Hill and Earthbound 1994, Kefka's ever-popular laugh note {which had already been used in Sonic Oddball Crackups in lieu of Knuckles' sniggering for intentional comedic effect}, etc.).
The ending. It ends with a bloodied Sonic plushie that appeared out of nowhere on Tom's bed.
In the sequel, our protagonist, despite writing in a diary, decides to write in abbreviations you'd be more likely to see in texting. Made even worse by him suddenly realizing his sister played the game and fell victim to X, yet he stillhas to write all that down and call out to his sister in that very diary.
Older Than They Think: It was revealed on October 12th 2023 that the very first Sonic.exe creepypasta actually predates the one commonly known today, having started out as a Happy Tree Friends edit of all things, then came to be a Spanish creepypasta dubbed "The Blue Pendrive". The revealed info can be found here.
Serial Numbers Filed Off: Some people tend to point out how many key plot points "Sonic.exe Round 2" borrows from another creepypasta, "The Case of Stitch". Two detectives (one male, one female) try to investigate a series of gruesome murders, the female investigator then disappears and the male protagonist meets the culprit in person and realizes he is powerless to stop them. "Round 2" follows the exact same formula, except the protagonists are siblings instead of friends and X replaces the eponymous Stitch as the main antagonist.
Due to the sheer quantity of Nightmare Retardant and an absolute torrent of a Cliché Storm of Creepypasta tropes, this story has this reputation among hardcore Creepypasta fans.
Too Bleak, Stopped Caring: The protagonists are idiots who endanger themselves and others through their acts, and the antagonist is an obnoxious Eldritch Abomination who can never be defeated.
Unintentionally Unsympathetic: Tom can be hard to sympathise with due to how idiotic his actions are (like playing a game even after he was repeatedly told to destroy it) and the fact that he cares more about fictional characters dying rather than his real-friend who probably died trying to save him, never considering about it until the end, which was still overshadowed by him worrying over Tails, Knuckles, and especially Robotnik.
The original video game adaptation of the Creepypasta by MY5TCrimson (which simulates Tom's experience) is more well-known and was often considered the superior experience by many, as you are the one experiencing the cat-and-mouse game with the demonic Sonic, as opposed to the contrived and idiotic human characters in the original story. Though the lack of proper gameplay, a lot of Nightmare Retardant moments and amount of similar fangames trying to piggyback on its success with various results somewhat tarnished the first adaptation as the time went on.
The remastered version has become much better received than even the first adaptation thanks to being geniunely scary with the involvement of featuring original art and music, as well as following the original creepypasta quite closely.
The title screen's split-second change is reduced down to just seeing Sonic's arm and X's red pupils in pitch blackness before disappearing. It's both more subtle and just a little easier to buy someone passing off as "just a glitch".
X's voice, which was added in Version 7 of the original game, is greatly reduced in the remaster, with him saying only one line right at the very end. As a result, the demonic Sonic's antics as well as the text boxes are much more eerie in the silence.
The voiceovers for X introduced in Version 7 of the original game can sound more ridiculous or over-the-top in a Crosses the Line Twice way than scary.
When X says "DIE" every time the player collects a negative ring.
When X catches Tails, he snarls "I will eat your heart", but the distortion of his voice makes the "heart" sound like "hat".
When X says "I will strip your flesh from your body." In the secret level of Robotnik's stage. The way he says it makes it sound like he is just so done with everything that it is hard to take seriously.