The Black Doom saga is one of the four games that's part of the Sonic 2D All-Stars collection. It reimagines the events of Shadow the Hedgehog in 2D, as Sonic is a playable character with his own storyline.
Like the other three 2D remakes of the 3D games, the Black Doom Saga is played as a typical 2D sidescroller like the original 2D Genesis games, complete with Sonic's trademark speed, platforming, enemies, obstacles, and end-bosses. Also included is Sonic Advance 3's tag-action system, which allows the player to earn different abilities depending on which one of Sonic and Shadow's friends they pick as their AI-controlled partner. The partners change or get omitted depending on which stage the player is in and what moral choice Sonic/Shadow made throughout their respective storylines. The stages' layouts and enemies also change depending on which moral choice the player makes; one stage would have only GUN soldiers to fight against while the other with the same theme but different layout might have aliens to combat against.
Sonic, Tails, Amy, and Cream stand on the top of a mountainside overshadowing Westopolis, as they came to view the arrival of the Black Comet. As they watched, the sky turns black, and an army of aliens appeared and started to invade the city. Just when Sonic and his friends were about to fight the aliens, a helicopter appeared as it landed and revealed the GUN army commander to the group. He tells them about Black Doom's plans to steal the Chaos Emeralds with his alien army, and gives them an assignment: Find the seven Chaos Emeralds before Black Doom does, and use them to kill him, and with him their own friend Shadow the Hedgehog. Shocked and reluctant, they asked why the commander would order them to kill their own friend, who helped them and the world in the past, but the commander refused to unveil why he hates one of Sonic's own friends, telling them that if they continue to sympathize with Shadow, the commander will deem Sonic and friends, the very heroes who saved humanity countless times, traitors to GUN, and would send his troops to kill Sonic and his friends on sight as punishment.
Thus, do Sonic and his friends (including the friends they'd encounter and team-up with along the way, Knuckles, Rouge, and the Chaotix Team, each of whom were also ordered by the GUN commander to kill Shadow or else they'll die as punishment for sympathizing with the black hedgehog) have to make a choice: Redeem Shadow and bring him back to their side at the risk of defying, and being hunted down and killed by, the GUN army, kill Shadow so that GUN wouldn't hunt down and kill them, or take the neutral route and race against Black Doom's alien army for the Chaos Emeralds.
Depending on the choices made, Sonic and his friends might face one of four main end-bosses: Black Doom in four of the five routes, Dr. Eggman in the two neutral routes, the misguided GUN commander in his mech-suit, Diablon, in the hero and pure hero routes, and Shadow the Hedgehog in the dark and pure dark routes.
As with the original 3D game of the same name as Shadow's, Shadow was by himself, alone, also viewing the black comet falling from the sky above Westopolis. As Shadow was about to walk away, he was then surprised by the appearance of aliens falling from the sky, invading Westopolis. Before Shadow could act against them, Black Doom appeared before him and ordered Shadow to collect the Chaos Emeralds. Because the reimagined Black Doom Saga takes place two games after the reimagined ARK Saga's alternate ending, Shadow only remembered Gerald and Maria in his past, but not Black Doom or why he knew him, due to his memory decaying from fifty years of his imprisonment. Shadow asks how Black Doom knows Shadow or why he's ordering him to collect the Chaos Emeralds, but Black Doom replied by saying that if he obey his orders, he will receive not only answers, but also a chance to succeed and surpass Black Doom as his potential heir to the Black Arms throne, destined to take Black Doom's place as ruler of his alien armies anytime he dies or disappears.
Thus, does Shadow have to make a choice: Put his past behind him and instead focus on Sonic and his friends, who redeemed him during the ARK Saga, gain his past at the expense of siding with Black Doom and killing his own friends, or take the middle-route and figure out what to do from there.
Depending on the choices made, Shadow may fight one of four main end-bosses: Black Doom in the hero and pure hero routes, the GUN commander in his mech-suit, Diablon, in four out of five of the routes, Dr. Eggman in the two neutral routes, or Sonic and his beloved friends in the dark and pure dark routes. Also included is a boss battle against Vector, Espio, and Charmy of the Chaotix Team in the pure dark route's "The ARK" stage, instead of the GUN Heavy Dog mech from the original 3D version of the Shadow the Hedgehog game.
This can only be unlocked if the player managed to complete all ten routes with both Sonic and Shadow. Also, unlike the original 3D version of the game, the Black Doom Saga's final storyline will have only Sonic as the playable character instead of Shadow.
Sonic, Tails, Knuckles, Amy, Cream, Rouge, and Shadow managed to collect all seven Chaos Emeralds as they face off against Black Doom, who reveals to the heroes Shadow's connection to Black Doom fifty years ago, and why the GUN commander hates Shadow so much: Black Doom helped Gerald, Shadow's original creator, in creating Shadow by transferring his blood, and in turn his Chaos powers, into Shadow's veins, giving him life. The heroes were shocked at the news, arguing that they don't care if Shadow was created by Black Doom this whole time, because Shadow is their friend and a free citizen with his own thoughts and emotions like any normal hedgehog on Earth. Black Doom, however, commented that Shadow is hated and feared for being Black Doom's creation, a murderer, and a potential heir to the Black Arms throne, built to succeed, surpass, and replace Black Doom as ruler of his alien armies anytime anything were to happen to him. He said to Sonic and his friends that they shouldn't be friends with a Black Doom spawn because to the GUN commander, anyone that dares sympathizes with Shadow is an enemy of GUN and the equivalent of Black Doom and his Black Arms army.
However, Black Doom offered them an alternative to their problems with GUN: Join forces with Shadow and Black Doom, so that they can get their revenge on the GUN army for turning them against their own friend, as well as the various bad people like Dr. Eggman, that have wronged them too many times in the past, and they can rule Earth and its people alongside Shadow, keeping their friendship with him for the rest of their lives. Sonic and his friends refused, saying that Black Doom would only do that because he's afraid of Sonic and company and their ability to overthrow Black Doom and turn Shadow against him, and he'd only do that to gain the very strengths he's afraid of for his own evil gains. As punishment for turning down Black Doom's offer, Black Doom mind-controlled Shadow, via the blood he transferred into Shadow's veins fifty years ago, into stealing the Chaos Emeralds from Sonic and friends, and ran away with Shadow and the seven emeralds. Running low on time, Sonic and his friends gave chase toward Black Doom through his Black Comet, and into his throne room, where he, Shadow, the stolen Chaos Emeralds, and the final battle against him lied.
In the Black Arms throne room, as the heroes arrived they saw Black Doom sitting comfortably on his throne, with Shadow standing in front of him motionlessly. They attempted to convince Shadow to break free of Black Doom's control over him, when Shadow slowly walked toward Sonic, choked him, and lifted him high in the air. Shadow couldn't remember anything, including his past, his friends, and even his own name and identity. Shadow then released Sonic, struggling with something inside, as he then floated in the air and powered up in a dark aura. Black Doom then revealed to Sonic and his friends that they were too late: Black Doom has complete control over Shadow via the blood he inserted inside the black hedgehog's veins. Black Doom then revealed that Shadow was not only his heir, but also his potential vessel. Black Doom knew that he grew too old, elderly, and in turn weak even to lead his alien armies or defeat any threat to his plans, even Sonic and his friends, and that he would eventually die from old age or be killed by either GUN, Sonic and his friends, or any other threat that dared to get in his way. So fifty years ago, he tricked Gerald into transferring Black Doom's life-blood into Shadow, so that anytime Black Doom dies, a piece of his soul within his transferred blood would possess and live on within Shadow's stronger, much younger body. He also needed the Chaos Emeralds to enact his other plan: By using the emeralds' powers to amplify his own, he used Chaos Control to warp the Black Comet into Earth's atmosphere, as it released tendrils that attached it into the Earth's ground. Sonic and company wondered what significance did warping the Black Comet into the Earth had, and Black Doom goaded the six into moving their limbs, to see if they can attack him. Sonic and his friends tried to move, but to no avail, as they were paralyzed by Black Doom's nerve gas. Black Doom knew that his comet wouldn't survive the impact into the Earth's atmosphere as it would burn up, so he used his potential blood-related creation, heir, and vessel, Shadow, to collect the Chaos Emeralds for him. Black Doom then controls Shadow and orders him to finish off his friends, while proclaiming that he was the one who created Shadow, and that he deserved all the credit, and with it full custody of Shadow.
Meanwhile, in the Space Colony ARK's computer room, Vector, Espio, and Charmy were watching helplessly from the window as the Earth was slowly being consumed by Black Doom's paralysis gas, while struggling to gain any information from the computer on how to stop Black Doom. As Vector banged on the keyboard, an image of Professor Gerald appeared on the computer, all over the world, and the Black Comet in front of Shadow, Black Doom, and Sonic and friends. Gerald regretted being tricked by Black Doom, and that he intended Shadow not to be the heir of Black Doom's throne as Black Doom wanted him to be, but rather a normal hedgehog with thoughts and a free will, destined to use his powers to protect innocent people and live out his own life the way his creation wanted to. Gerald then instructed Shadow to use the ARK's Eclipse Cannon to destroy Black Doom and his comet, because he built it anytime invaders like Black Doom would come to attack Earth. After doing so, Gerald suggested that Shadow forgets him, Maria, and his tragic past anytime they die, and instead live a free life as a normal hedgehog, and making friends that, unlike Black Doom (who would use Shadow as his vessel and potential weapon), would actually care for him and treat him like a normal hedgehog and a free citizen. Maria then appears and tells Shadow the same thing her grandfather, Gerald, said to him. The screen then disappears.
Despite Black Doom's control on Shadow, the black hedgehog would shed a tear over everything Gerald and Maria said, and slowly re-remembered how much he cared for the new friends he made that helped redeem himself during the events of the ARK Saga. Temporarily and somewhat breaking free of Black Doom's control over him, Shadow fired six balls of energy at Sonic and his five friends, freeing them from, and providing them immunity from, the paralysis gas, as well as giving them enough energy to combat Black Doom. Black Doom then regains control over Shadow, who knocks out Sonic and friends with a Chaos Blast. However, Sonic and friends got back up, and explained to Black Doom that he maybe Shadow's creator, but he's not his true family. Gerald and Maria provided Shadow with the love and care Black Doom robbed the black hedgehog of, and even if Gerald and Maria are dead because of Black Doom and his alien armies, even if the GUN commander hates Shadow for the crimes Black Doom himself, not Shadow, committed fifty years ago, Sonic and the gang will always be Shadow's real family no matter what. And, as Shadow's true family, they will save Shadow from Black Doom's control, power, and influence, even if it means being deemed traitors to GUN and thus be hunted down and killed on sight by the GUN commander's troops as punishment for merely saving his life, once this is all over. Disgusted by Sonic and friends' rousing speech about how they're Shadow's real family, Black Doom then used the Chaos Emeralds to transform his slave and vessel, Shadow, into Hyper Shadow, while Sonic would absorb some of the Chaos Emeralds' powers to become Super Sonic. Super Sonic and Hyper Shadow would fight each other outside the Black Comet, above a gas-infected Westopolis, while Tails, Knuckles, Amy, Cream, and Rouge fought Black Doom within his throne room. The two battles were long, difficult, and gruelng, but Sonic's five friends managed to defeat Black Doom and escape the comet, running toward Tails' plane, the Tornado, to assist Sonic, who defeated Hyper Shadow.
Black Doom, in his giant, monstrous Devil Doom form, then appeared, grabbed the defeated and comatose Shadow, and ate him as punishment for failing against Sonic, regaining the blood and power he transferred into Shadow fifty years ago. Devil Doom then asked Super Sonic why he and his friends would sympathize with the very Black Doom spawn and murderer the GUN commander despised so much, and Sonic said that Shadow is a friend who can still be redeemed for everything Black Doom did fifty years ago. Super Sonic, aided by his friends flying the Tornado, would fight Devil Doom in one last battle to determine Shadow's and all of Earth's fate, and after a long, grueling battle, Super Sonic and friends would win. After the battle, Sonic would break into Devil Doom's stomach and free Shadow from the inside-out, as a defeated Devil Doom vanished into oblivion. Super Sonic handed Shadow to his friends' care, as he used Chaos Control to warp the Black Comet out of Earth's atmosphere and back into outer space, where Sonic would finish off Shadow's own job, given to him by Gerald and Maria, of using the Eclipse Cannon to destroy the comet.
Back at GUN headquarters, as the commander and his president and troops viewed the final battle and the destruction of Black Doom and his comet, they come to realize that Gerald intended to do good despite his crimes during the ARK Saga, and the commander's viewpoint of Shadow would change, realizing that Sonic and his friends were actually right, that the black hedgehog was just an innocent victim caught in the middle of the war, as well as a normal, free hedgehog who had Sonic and friends to care for him as his friends. The commander was confused and upset over whether or not Sonic really is right, but the president comforted him, saying that Sonic and friends cared for Shadow as a friend and wanted him to leave his past behind for the present, and suggested to his commander that he does likewise with everything that happened fifty years ago as well.
Meanwhile, on the ARK, after destroying the Black Comet with the Eclipse Cannon, Sonic, in his normal blue form, tiredly walked to the computer room, where he was reunited with a relieved and happy Chaotix Team, who watched the final battle from the ARK and were glad that Sonic and friends not only managed to survive, but defeat Black Doom and save Shadow and all of Earth. Sonic then received communications from friends on Earth via the earpiece he and his friends use whenever they were apart, telling him that he should come because they have a problem with Shadow. Sonic, and with him the Chaotix Team, who also wanted to help Sonic, Shadow, and the rest of their friends, left the ARK via an escape pod as they fell into the Earth's atmosphere, into Westopolis, where the four would reunite with Sonic's friends. They revealed to Sonic and the Chaotix Team that Shadow is standing on a hill, looking at a photo of Gerald and Maria while sad, and that they needed his and the Chaotix Team's help in comforting Shadow. Sonic, Vector, Espio, and Charmy agreed, as they and their friends all walked to Shadow.
As they arrived, Sonic and his friends saw Shadow looking at the photo of his deceased creator and childhood friend, all sad because of his past. Sonic snatched the photo away from Shadow, crumples it, and feeds it to Vector as he chewed and swallowed the photo. They tell Shadow that he's free from his past and Black Doom, and that he can now live freely as a normal hedgehog with a heart and free will. Shadow disagreed to his friends, saying that Black Doom's soul lives on within his blood, which he transferred into Shadow's veins fifty years ago. As long as Shadow has Black Doom's blood, Black Doom will return and attempt to possess Shadow again like last time. He then suggested that anytime that were to happen, his friends would have no other choice but to kill him. Sonic and his friends declined Shadow's suggestion, saying that Shadow is the Ultimate Life-Form and therefore too powerful to allow Black Doom to possess him again, saying that anytime he returns to possess him, Shadow will have to fight Black Doom himself, and his friends would help him anytime he has to fight Black Doom within his mind. Shadow, glad to have "a bunch of suicidal fools" for friends, walks with his friends, leaving a heavily damaged Westopolis to celebrate Sonic and company's victory and Shadow's freedom from Black Doom.