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Shadow is acrophobic.

  • He's afraid of heights. It's brought up how high they are sometimes. Allies often say "It's a long way down" and "Look below you". At one point Black Doom even mocks Shadow in Air Fleet and asks him "Surely you're not afraid of heights?". And it makes sense too - Shadow has fallen from the ARK twice; a lot of his bad times involve being in high places. In fact, the most likely thing you are to die from, is something height related. Shadow even has an animation where if he comes too close to an edge - sometimes even if you may be running fairly fast at the time - when he freezes up and flails his arms, keeping you from running over the edge.
    • It also makes a great contrast to Sonic's inability to swim and his perceived aquaphobia.

The game is actually Shadow's Self-Insert Fic
  • After the events of Sonic Heroes, Shadow, after (somehow) getting his memory back, was bored as well as jealous of Sonic's popularity. To alleviate this, he writes his own stories in an attempt to make himself look cooler! This is one of his crazier stories.

    Why are crazy aliens be involved? So Shadows would have the excuse of "Aliens made him do it". Why does the grass suddenly explode in the intro? Explosions make things awesome! Why does this game allows Shadow to wield guns and drive motorcycles? He wants to look badass. Why is Sonic dying at Shadow's feet in the Pre-title cutscene? The Fic is a Revenge Fic! Why is this the only Sonic game where you're allowed to harm the human soldiers who are also lead by a Hedgehogist(?) jerk? Because the GUN soldiers killed Maria, making them acceptable targets for him. Why are characters swearing like Shadow is? They are Out of Character because he only really knows his compatriots on a surface level (e.g. Eggman is a buffoon; Tails is childlike and afraid of the dark; Rouge has breasteses). Why does the game have multiple paths that are meaningless in favor of Shadow being the good guy? He doesn't know what he wants to do with the story, but he does want everyone to see him as being as cool as or even cooler than Sonic.

"Goodbye, forever" was actually Shadow's note of staying on the ARK
The ones we see from now on are Androids.

Shadow regaining his hatred for humans was due to Prof. Gerald's conditioning of his mind 50 years ago.
The reason Shadow had regained his hatred for humanity as learned in the opening scene of the game was due to the fact Prof. Gerald Robotnik had reprogrammed Shadow's mind into hating them after Maria's death at the hands of G.U.N. After Shadow realizes that Maria wanted him to help humanity, he made a Heel–Face Turn and helped Sonic save the world, which led to him falling into earth. After Shadow was awakened with amnesia, not to mention after the events of Sonic Heroes, the images of Maria being killed at the hands of a G.U.N. soldier had appeared in his mind, and it turns out that the brainwashing Prof. Gerald had done to him 50 years ago still had an effect on him, though to a lesser extent. In the last story, however, Shadow's hatred for humanity was remedied for good after he resolved to put the past behind him and saved the world again from the Black Arms.

Black Doom is subtly using mind control to influence Shadow during the entirety of the game.
That would largely account for why Shadow blindly trusts him at the beginning of the game rather than talk to someone he already knows (such as Rouge or Sonic) and why he takes orders from Doom so willingly in many of the Dark missions. In one of the last cutscenes, Shadow is shown to have a resistance to Doom's mind control, so he may have built up a tolerance towards it. Doom's control over Shadow is weaker than his control over the Black Arms because Shadow only has some of his DNA and is not a member of the alien species himself.

E-123 Omega sang Waking up along with Julien-K.

Blaze the Cat is secretly involved with the events of the game.
She brought the Chaotix to the ARK's main computer room, to recover some data using five secret disks and used the Sol Emeralds to power up the Eclipse Cannon to destroy the Black Comet. She is the Chaotix's client.
  • Incidentally, both this game and Sonic Rush released on the same day in North America and Europe. Was this more than just a mere coincidence? Also you're missing some points. If Sonic Rush happens at the same time as Shadow the Hedgehog, then how come Blaze never met Shadow during her search for the Sol Emeralds? Alternate Sonic dimensions maybe?
  • Alternatively, Silver the Hedgehog is involved instead. He travelled to the past as the Chaotix' secret client in order to prevent Iblis from returning since he believes it is secretly linked to the Black Arms, when it is not the case. Even after the Black Comet does get destroyed in the end, Iblis keeps returning, proving Silver wrong in the end.

Eggman lied; Shadow's not the original.
Eggman used data from the ARK to attempt to construct new Shadow minions, as they were the only thing of manageable size which could use Chaos energy and put Sonic on the ropes, but they were incredibly hard to get right and he ended up with hundreds of "template" models, the androids, which each have a small adjustment towards the overall intended product. The likes of Shadow seen these days are the first ones Eggman tried to make, which were too independent and used their advanced capabilities to cause problems, resulting in him doing things such as sealing them away in cold storage. The later "Shadow androids" deviated only slightly from a controllable template, making them safer in the long run.
  • The amnesia is due to "Shadow" not having any memories of his own, just those Dr Eggman knows about and could program in. He wasn't even finished adding them until he decided to put him in the tube. He doesn't think about things that would prove he's an android like needing to eat because the A.I and his own identity crisis won't let him realize that.

Egg Dealer isn't a battle mech
Dr. Eggman originally built the Egg Dealer as an attraction for one of his casinos, but he needed something immediately on hand after a few other designs didn't work and he found himself suddenly pressed for time. All he had was Egg Dealer, so he changed the reels out for weapons, Pawns, and Shadow Androids (Rings was the only holdover from its intended purpose) and repainted it, all in great haste. That's why it's unfinished and so easy to defeat: He just didn't have time to fit any other weapons onto it. All that guff about "MY STRONGEST CREATION YET!" is bravado: He's lying through his teeth and he knows it.

The canon path
First is Westopolis: Normal. At the beginning, Shadow doesn't really care about the GUN vs. Black Arms conflict, and just wants to get the Chaos Emeralds and get his memories back. After all, in the opening and trailer we see him fighting both aliens and GUN. At the end of the stage, Black Doom teleports him to Glyphic Canyon to punish him for not following him. This leads to Glyphic Canyon: Dark, as Shadow decides that angering Black Doom further is more trouble than it's worth and that he should play along for now. Afterwards is Cryptic Castle: Hero; Amy and Cream's plight subconsciously stirs Shadow's memories of his failure to protect Maria, and he helps them out. This lines up with Cream's quote in The ARK on Expert Mode: "Thank you so, so much for rescuing me the other day!" Having gotten sidetracked from his original goal twice now, he gets back to pursuing Eggman with Sky Troops: Normal. This leads him to Iron Jungle, where Shadow discovers his android copies. Panicking, he helps Eggman in order to get the truth out of him by doing Iron Jungle: Dark. Before the subsequent boss fight, Eggman claims to Shadow's face that he is an android copy of the original Shadow, lining up with a quote late in the Devil Doom fight where he admits to having lied directly to Shadow on this matter: "This might be the last chance I have to speak to you, so... what I said, about having created you? It was all a lie." This also brings Shadow to the Black Comet for the final level, where The Last Way clearly and explicitly takes place. Now hoping to get answers out of Black Doom, Shadow does Black Comet: Dark and faces the Diablon mech in battle, lining up with the GUN Commander's quote in Space Gadget on Expert Mode: "First, I want to... apologize, for the other day..." His wording here sounds more like he is apologizing for a specific incident than his general treatment of Shadow, which could only be the Diablon fight. Having acquired all of the Chaos Emeralds, Shadow decides to learn the truth about his past and faces down Black Doom once and for all, as depicted in The Last Way.
  • Alternatively Shadow decides to help his old partner Omega in Iron Jungle which still leads to Eggman claiming Shadow being an Android but Shadow instead teleports to the Ark where the GUN commander attacks Shadow unprompted. The Commander's apology wouldn't make much sense if Shadow was allied with the Black Arms it had to be something unprompted. In addtion it's hard to imagine the commander being able to get back to Earth upon getting his ass kicked. While here he's uninjured and close to the ARK's teleportation system. Following this Shadow ignores Vector's request in Cosmic Fall and heads straight for the Emerald where Eggman tries to trip Shadow up by claiming he was created by Gerald. Shadow wins but spares Eggman however receiving conflicting stories on his origin and not being given any reason to outright distrust Black Doom he decides to head to warp to the Black Comet which is currently right next to the ARK leading to the final story.

The GUN Commander was the son of the commander who lead the Space Colony ARK raid.
Along with explaining why he wasn't a casualty, it also explains why the Commander blames Shadow of all people for the massacre or even joined GUN. He doesn't want to accept what his father did and wants to believe he and GUN are a force for good, and his father would've been quick to justify what he did to his son. It's also why he was the only survivor. Not being able to blame his father or his life legacy, the GUN Commander makes Shadow his scapegoat on the reasoning he was the motive behind the massacre. Realizing that Gerald Robotnik was a good man before being driven insane at the end and that he made a way to save the Earth from his mistake convinces him he had no right to blame Shadow and he works to put the past behind him and Shadow, eventually leading to Shadow becoming a member of GUN after they bury the hatchet and come to appreciate one another. Rouge being associated helped with the reconciliation.

Shadow is a Cyborg.
Him being an android is only partially false. Eggman mentions rescuing him, however it still doesn't explain how he survived atmospheric re-entry. Maybe he's tougher than even Sonic thought, or maybe he was one foot in the grave. Eggman found him and rebuilt him in order to save his life. When he claims he "made" him, it's more he re-made him. His amnesia is due to part of his head, possibly even his parts of his own brain matter having to be replaced by cybernetics. Why doesn't the doctor put some sort of mind control device? He already has androids who rebelled, and while bonding animals to his robots gives him enough know-how on giving people an Emergency Transformation, this isn't SATAM and he can't physically convert people into robot slaves...yet. Alternatively he was working on a mind control chip, but Shadow was broken out by Rouge and Omega before he could put it in. Being partially mechanical may play into how he could ignore Black Doom's mind control, though that may also be just him being the Ultimate Lifeform/sharing the same blood as Black Doom.

Doom's Eye is the real Black Doom, not the Horned Humanoid.
The starfish is the real creature, while Black Doom is actually an illusion. His telepathy is strong enough to convince people it's the real thing. You don't see Doom's Eye when fighting regular Black Doom; he's cloaking himself in the illusion and using the attacks as a starfish. Why bother with an illusion if he's just as powerful as a starfish? Simple; he wants to come off as intimidating. The only time he's actually bigger than Shadow is as Devil Doom; using the Chaos Emeralds he can generate a massive new body to use against Super Shadow. Of course, it's also equally possible that Black Doom as we see him is flesh and blood, however Doom's Eye could still be the real thing; vanilla Black Doom and Devil Doom are just an empty vessel Doom's Eye puppets in order to interact with people.

The entire game was a "Groundhog Day" Loop designed by Black Doom.
The intro is the only part of the game where Shadow isn't under Black Doom's control (until you unlock Last Story) After that, he's trapped and regardless of his decisions, Black Doom will reset the timeline once you get any ending. That's why all the cutscenes are reused for different scenarios. Black Doom was just recycling footage to use when messing with Shadow's head, because he knows that Shadow won't notice, and that he'll remember nothing when Black Doom resets the timeline.

Its shown in one or two cutscenes that Black Doom can even create physical locations from Shadow's memories hence why The Doom and Lost Impact exist, with both existing to break Shadow further. Even in timelines where he sides with Black Doom, the timeline resets because Black Doom knows that Shadow will prove to be a liability to him when the time comes to put his plan in motion. This is further supported by how most of the paths have you either side against him directly or indirectly on the Neutral routes, or how Shadow betrays Black Doom during the Pure Dark-Hero in order to rule the universe himself.

Lastly Black Doom is able to use Chaos Control to bring down the Black Comet to Earth, and can use this skill as Devil Doom. In addition, there are 326 timelines that the player can go through, though thankfully they only have to go through 10 of them to unlock Last Story and free Shadow from Black Doom's grip.

Amy charmed Shadow into not being evil anymore.
In the path "Miracle of Love", Shadow performs the Dark mission for the first two levels, then from the third onwards, he always does the heroic thing. What would be the third level if you go this route? Cryptic Castle, where the hero character is Amy. Who is a hedgehog, just like Shadow. Similarly, in the route "The Ultimate Confrontation", where instead you also do the dark mission for the last level, leading to the boss fight with Sonic, one could imagine the two of them competing for Amy's love.

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