Main Story
Sonic the Hedgehog, everyone's number one blue blur rushes through Green Hill Zone, a thriving lush field of greenery and grass which is now overrun by sand and robotic worms. The blue blur, having received a call from Tails the fox about an attack on the city, rushes to aid his best friend. However, when he tries to confront his long time enemy, Doctor Ivo "Eggman" Robotnik, he is suddenly attacked by four of his old foes, Shadow, Chaos, Metal Sonic and Zavok, along with a mysterious new enemy. With their combined power, the five villains utterly crush Sonic, to Tails' horror and Eggman's delight. Following his ultimate victory, Eggman proceeds to effortlessly conquer Earth.Fast forward six months to where the War to Take Back the Planet is now in full force. The Resistance, led by Knuckles and including the likes of Amy Rose, the Chaotix in Vector, Espio, and Charmy, Silver the Hedgehog, and Rouge the Bat, find themselves in a difficult position as Eggman's forces seem unbeatable and the people are losing hope and giving into despair. Tails has gone MIA after Sonic's defeat, Silver thinking he's lost his mind over the guilt of being unable to protect Sonic, and Sonic is presumed KIA. Espio supports him as it is clear the Resistance needs to make their own miracle to win the war, and Silver suggests that to restore morale among the people, they have to show that strength comes from more than just numbers. Charmy then mentions a new recruit joining them, Silver saying they're a survivor from the City, and Amy accesses their file on the Resistance's database. Shortly thereafter, Knuckles arrives and gives his Resistance members a briefing on their current situation, before the new recruit arrives and is welcomed into the Resistance's ranks, armed with a Burst Wispon, and the Resistance prepares for their next move.
Word soon comes in that Sonic is still very much alive, but is currently incarcerated, whereabouts unknown at the moment, but the location is in space, so the Resistance will need to "borrow" an Eggman Fleet shuttle from the Chemical Plant Spaceport to head up to rescue him. Although the Resistance spots the same enemy that took down Sonic at the Spaceport, they are able to avoid him and secure a shuttle.
Meanwhile, Tails is back in the City, trying to repair a severely-damaged E-123 Omega when he is confronted by Chaos. As Tails cowers in fear and cries out for Sonic to help him, Chaos lunges an arm at Tails, but hesitates when a portal suddenly opens, and Classic Sonic runs out of it and dispatches Chaos in short order. When Tails realizes it is Classic Sonic who saved him, remembering him from the events of Sonic Generations, he surmises that whatever new power Eggman is using is what brought Classic Sonic to their dimension to help protect it. Together, Tails and Classic Sonic head out to find Eggman and whatever new power he is using against them.
Back with the Resistance, they are contacted by their spy, Rouge, who reports that Sonic is incarcerated on the Death Egg, pending execution as Eggman wanted Sonic to see his completed Eggman Empire before banishing him into space. However, Eggman caught wind of the Resistance trying to rescue Sonic, and pushed his execution ahead of schedule. With time not on their side, the Resistance storms the Death Egg to locate Sonic before his termination. The new recruit manages to cause enough of a ruckus that, just as Zavok arrives to escort Sonic to his demise, a momentary power flux frees Sonic from his shackles, allowing him to face Zavok and the Death Queen in combat and defeat them. Zavok mysteriously vanishes after collapsing in exhaustion, much to Sonic's puzzlement, but he quickly forgets about it as he makes his escape to the Death Egg's hangar deck, rescuing the new recruit along the way. When Knuckles contacts the recruit for a sit-rep, Sonic reveals his presence, much to Amy's relief that he's alright, before Sonic and the recruit use an Eggman Fleet shuttle just about to take off to return to Earth and rejoin the Resistance.
Once they rejoin the Resistance, thereby restoring morale with the people when they learn Sonic is alive, Knuckles explains to Sonic that Eggman has established his main munitions factory, the Arsenal Pyramid, in Green Hill Zone, and if the Resistance is to launch an attack on Metropolis, the factory has to be destroyed first and foremost. Sonic is assigned the duty to take it out with the new recruit, despite there being some concern that the recruit is still shaken up from what happened on the Death Egg. In the end, thanks to Sonic giving them a much needed boost to their self-confidence, the new recruit and Sonic are successful in destroying the Arsenal Pyramid, cutting off Eggman's main source of his warmongering.
However, shortly after Sonic and the new recruit's triumph at the Arsenal Pyramid, Silver reports in that he and Resistance forces in the Mystic Jungle are under attack by the new enemy that kicked Sonic's butt at the start of the war. Seeing a chance for Revenge, Sonic heads to the Mystic Jungle to rescue Silver, arriving just in time to stop the new enemy's death blow to Silver after he was bested. The new enemy is not at all surprised to see that Sonic is still alive after the thrashing he gave him previously, and is more than ready to give him another pounding. However, he is courteous enough to introduce himself to Sonic as "Infinite", but refuses to disclose the source of his power to Sonic, instead using said power to drag Sonic into another fight. Though Sonic puts up a much tougher and fiercer fight compared to their first match, Infinite decides Sonic is not worth his time to finish off after overpowering him and takes his leave.
Back with Tails and Classic Sonic, they make their way through Green Hill Zone until they happen across Eggman and Infinite in conversation with each other, as Infinite finishes off destroying all the prototypes of the Phantom Ruby he had retrieved from Eggman's lab in Mystic Jungle before engaging Silver and Sonic. Though Eggman is pleased that the lab is now on lockdown, he then inquires about Sonic, only to learn that Infinite spared him after their last confrontation, much to Eggman's fury, especially when Infinite taunts that he handled Sonic way much better compared to how Eggman has lost to him repeatedly over the years up until now. After Tails and Classic Sonic are nearly spotted, Infinite asks about if they are on track for their endgame against the Resistance, and Eggman assures that in a short time, the Resistance will be wiped from the face of the Earth, and a glorious Eggman Empire will rise from the ashes of the old world, while Infinite agrees that the Resistance will bow to the Phantom Ruby's power in due time. With that set and done, Infinite departs, allowing Classic Sonic to make his move and attack Eggman. Though he attempts to escape, Eggman nevertheless fights Classic Sonic using both a swinging sawblade similar to his original weapon from Green Hill Zone in Sonic the Hedgehog (1991), and bringing the Egg Dragoon in when that is destroyed, but Classic Sonic overpowers both. Eggman later crashes the Egg Mobile into the footpath, but is not at all disappointed in his defeat, gloating to Tails and Classic Sonic that his endgame that is taking place in three days will wipe them all out, refusing to disclose the details to Tails when he asks, saying "You know what they say: The anticipation of the end is worse than the end itself.", before taking his leave.
At the Resistance HQ, word comes that the Eggman Army has broken through the Resistance's defensive lines in the City and are attacking in force. There are still civilians trapped and need to be evacuated, but there are no forces available to assist as Espio reports that he's engaged in Seaside Hill and can't send backup, a soldier from the Resistance's Eighth Unit reports that his forces are pinned down by heavy enemy fire and can't help either, and Sonic and Silver also can't assist, as they're still recovering from fighting Infinite in the Mystic Jungle. With no choice, Knuckles sends the new recruit in to help clear an evacuation route for the civvies, and thanks to their efforts, not only is an escape route opened up, but the Resistance soon has the enemy in full retreat, earning the new recruit commendations from Sonic personally.
As for Tails and Classic Sonic, they have reached the Mystic Jungle and are still looking for Sonic. Around this time, Rouge detects their lifeforms and Knuckles sends the new recruit to investigate. Upon reaching the area outside Eggman's lab where Sonic and Silver fought Infinite earlier, the new recruit finds that Infinite had dropped one of the Phantom Ruby Prototypes when battling Silver and picks it up, causing it to resonate with them, before Tails and Classic Sonic arrive and rendezvous with them. The new recruit takes them back to Resistance HQ, where Tails is reunited with Sonic at long last. Sonic also has a happy reunion with his Classic counterpart, as he mentions that "it's been generations since I saw you." Tails then explains about Eggman's endgame set to take place in three days, but Sonic is sure they can handle it no problem. It is then that Vector breaks in to report that Shadow is attacking the City and the Resistance forces there and they need reinforcements. Sonic heads in to personally deal with his arch-rival in the Ultimate Life Form, but just as Sonic confronts him and Shadow moves to attack, Chaos Control suddenly kicks in and another Shadow swoops in to roundhouse kick the one about to attack Sonic away, causing it to fade away similar to Zavok earlier. The Shadow that rescued Sonic is revealed to be the authentic one and reveals to Sonic that the Shadow the real one just defeated was a fake, a Replica created by Infinite using his new powers with the Phantom Ruby. Sonic is still convinced that they have a means to beat it and still win, despite the circumstances.
In the meantime, Knuckles notices that the guard around Metropolis has diminished greatly. Though Espio believes they are regrouping somewhere else, Knuckles decides to take advantage and launches "Operation Big Wave" to take Eggman's capital in one fell swoop. Unfortunately, Infinite arrives and throws the Resistance's plans into disarray, causing massive casualties, and forcing the Resistance into retreat before they are completely wiped out. During the withdrawal, the new recruit runs into Infinite, who confronts them after recognizing them as the Sole Survivor of when he wiped out their unit in the City a couple of months earlier and let them escape out of Cruel Mercy when he saw how terrified they were of him. Taunting them as to if they are going to run away again or die at his hands, the new recruit backs away in abject terror, but remembering some encouraging words from Sonic, they soon steel their resolve and tell Infinite to Bring It. Unimpressed, Infinite fights them, but although he is beaten, he tries to kill them using his Phantom Ruby power. Just as the new recruit is about to be slain, their Phantom Ruby Prototype overrides Infinite's power and saves them. Surprised and suspicious of this, Infinite still overpowers them before sparing their life, assuring them that their life is forfeit in two days anyway, before taking his leave.
With "Operation Big Wave" having been a bust thanks to Infinite, the Resistance turns their attention to finding a weakness in Infinite's Phantom Ruby. After Tails and Classic Sonic infiltrate the Chemical Plant Zone and find Eggman's main database, they learn that the Phantom Ruby requires a vast amount of energy to run, which can only be supplied by the Death Egg. Thus, if the Death Egg is destroyed, Infinite will be much weaker. After Sonic and the new recruit deal with a stronger Metal Sonic Replica that was attacking the City in the meantime, the Resistance sets into motion their plan to take out the Death Egg. First, the player's avatar creates a distraction to draw Eggman's forces away in Green Hill Zone, taking down the Death Crab in the process. With the distraction having worked, Sonic infiltrates the Chemical Plant Zone to shut down the Death Egg's defenses, allowing Classic Sonic to infiltrate the dreaded battle station and cause enough damage to destroy it, much to Eggman's frustration. Not at all annoyed by this setback with only a few hours left before his endgame goes into effect, Eggman orders Infinite to fall back to regroup, and though Infinite voices his contempt about this "tactical retreat", Eggman overrules him out of anger at his disrespect.
With the Death Egg destroyed, the Resistance believes that they have the upper hand now and launch a second siege of Metropolis to capture Eggman's capital. However, when Sonic and Tails find Eggman, Infinite reveals his Phantom Ruby powers are not weakened in the slightest as he prepares to banish Sonic to Null Space. Though the player's avatar tries to save Sonic, both are pulled into the void, while a shocked and confused Tails is told by a smug Eggman that he anticipated that the Resistance would go after the Death Egg, so he built a backup reactor for the Phantom Ruby under Metropolis as a safety measure. As the Resistance's air forces clash with the Eggman Fleet in the skies over Metropolis, Sonic and the player's avatar are able to escape Null Space and return to the fight, just as the Resistance is gaining the upper hand. When they confront Eggman, he's shocked and stunned that they escaped when he thought it impossible to escape the Phantom Ruby's Null Space. Nevertheless, Eggman assures Sonic that this changes nothing as he will have the last laugh before retreating with Infinite to his final stronghold, the Eggman Empire Fortress, leaving Metropolis to finally be captured by the Resistance.
With only a few hours left before Eggman's endgame goes into effect, and with their morale at an all-time high, the Resistance launches their final assault against the Eggman Empire Fortress. With Sonic, Classic Sonic, Tails, Knuckles, Amy, Rouge, Shadow, Silver, and the Chaotix leading the ground infantry, they charge into the fray, blasting and fighting their way past the hundreds of Replicas facing them until they reach Infinite. As the power-mad jackal prepares to kill all of them, he is momentarily interrupted by the return of a fully-repaired and operational E-123 Omega, looking for a little Revenge of its own. Fed up with the opposition before him, Infinite launches Eggman's endgame immediately, using his Phantom Ruby to summon a virtual Sun to drop on the Earth and vaporize everything that dares to stand against the Eggman Empire in one fall swoop.
It seems the Resistance's efforts have come to naught and been All for Nothing, until Tails notices the player's avatar's Phantom Ruby Prototype reacting. After asking for it and noticing it go dormant in his hand, Tails realizes that the prototype is attuned to the player's avatar as Eggman mentioned the defective prototypes could only record the DNA of the one that triggered them, meaning the player's avatar may be able to stop the virtual Sun using their prototype. Deciding it is worth the risk, the player's avatar makes their way to the top of the Imperial Tower and launches into the virtual Sun, all while Infinite and Eggman taunt that the Resistance's time is up and it is time to make peace with their fate. As the virtual Sun makes its decent, the Resistance watches in concern and fear as it gets closer, closer, closer...
Then, all of a sudden, it disappears. The Resistance cheer in having been saved from total annihilation, while a flabbergasted Eggman goes to investigate what stopped his endgame, discovering an exhausted player's avatar collapsing after having expunged their Phantom Ruby Prototype to stop the virtual Sun, the prototype shattering and the shards vanishing after having used up all its energy. Eggman is in disbelief, as he thought all the prototypes had been destroyed by Infinite earlier, but Tails lets him know he was Hoist by His Own Petard. With their morale restored, Knuckles orders the Resistance to resume their assault.
Sonic himself goes directly after Infinite while the Resistance air arm draw as much fire off of him as they can before being forced into retreat. Their efforts pay off as Sonic reaches Infinite, who gloats that, while he may still be weakened from launching Eggman's endgame, he's still powerful enough to take down Sonic. Infinite soon regains his full power, but before he can finish Sonic off, the player's avatar intervenes, drawing Infinite's attention while shooting him the most hateful Death Glare before joining Sonic to take the power-mad jackal down once and for all. Overpowered by their Double Boost, Infinite believes This Cannot Be! as he can't be defeated, only to be given a good "The Reason You Suck" Speech from Sonic over how he was beaten. Moments later, Infinite is drawn back towards the Imperial Tower against his will, before Eggman appears to warn Sonic and the player's avatar that his plans just when into overtime.
Unsure of what Eggman is up to, the Resistance decide their next move is to take out the backup Phantom Ruby reactor at the heart of the Eggman Empire Fortress. After Classic Sonic finds a back way in, Sonic and the player's avatar enter the tower and make their way to the reactor. After destroying the three Phantom Ruby energy siphons keeping the reactor stable, sending it into overload, Sonic and the player's avatar make their escape and regroup with Tails and Classic Sonic. Sonic immediately believes that they've won the war with the reactor destroyed, but he was Tempting Fate, as Eggman appears with his final trump card: The Death Egg Robot, powered by the original Phantom Ruby, which is creating thousands of Replicas to try and overwhelm the Resistance. Refusing to give up so easily, despite Eggman's taunts and how he will still see his Eggman Empire be victorious in the war, Sonic, Classic Sonic, and the player's avatar charge in to take down Eggman and the Phantom Ruby once and for all.
Though Eggman puts up a fierce defense against the trio, they are soon able to weaken the Death Egg Robot to the point they unleash their combined finisher, the Triple Boost, on it. Impaled with Extreme Prejudice by the Triple Boost, the Death Egg Robot is crippled beyond repair and begins to self-destruct. It would be a miracle if Eggman survived the finisher, never mind the explosion, but the villain has survived worse fates...
With Eggman's latest machine and the mad doctor defeated and the Phantom Ruby finally destroyed, Eggman's forces fade away, leaving the Eggman Empire ruined and earning the Resistance a hard-fought victory. However, Classic Sonic disappears from the realm to return to his own as a side effect of the gem's destruction. The player's avatar leaves the Resistance as they begin plans to rebuild society, meeting Sonic along the way before they both depart for new adventures.
