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Book One: Gatherings
Chapter 1: Echoes of KryptonYears ago, on the distant planet of Krypton, its inhabitants went to war against the Shi'ar Empire that entered their galaxy and invaded their planet. Within six years, the Kryptonians repelled the Shi'ar through their powerful technology thanks to the efforts of General Dru-Zod, the head of the Kryptonian Defense Force, who broke the siege aided by the new weaponry developed by Krypton's most brilliant scientist, Jor-El, Zod's longtime friend. With the Shi'ar defeated, the Shi'ar Emperor Kral'Nor was overthrown and exiled by a group of Shi'ar that opposed the war and the expansion. The New Shi'ar Empire quickly negotiated for peace and ending the war. However, Zod is later accused for war crimes of destroying Shi'ar warships that were about to surrender. Judged by Krypton's Council of Twelve, of which Jor-El is a part of, Zod justified that his actions were necessary to defending their planet through absolute force and doesn't show any remorse for his actions. The Council sentenced Zod to be exiled into the Phantom Zone. Following the trial, Jor-El present his findings concerning the possibility of Krypton's imminent destruction. However, the Council ignores Jor-El's warnings after Brainiac, Krypton's omniscient central computer created by Jor-El, dismisses Jor-El's findings and explains that Krypton is only undergoing a planetary shift. But Jor-El soon learns directly from Brainiac that it lied so that it could secretly download himself into a satellite and escape the planet's destruction, rather than be ordered to waste time preparing an evacuation plan. According to its programming, the survival of Krypton's knowledge is more important than that of its people. Jor-El, however, stops the download and takes all the knowledge Brainiac had before shutting the A.I. to prevent its escape. But as Jor-El leave, Brainiac had already issued an upload command. Jor-El returns to his home and warns his wife Lara that Krypton will explode in only a matter of hours. Jor-El quickly makes preparations for his back-up plan: to save his baby son, Kal-El, by sending him to Earth in a small one-person spaceship. With little choice left, Kal-El's ship is launch moments away as Krypton explodes. On Earth, at the Xavier Institute, Professor Charles Xavier and Erik Lensherr argues about humanity's acceptance of mutants; in which the former believes in coexistence between humans and mutants while the latter strongly believes that humanity will fear and loathe mutants and, inevitably, wage war on mutantkind; in which Lensherr intends to fight it. As Xavier tries to reason with his friend, he suddenly senses Krypton's destruction and its people's death cries. Although Xavier is disturbed, he couldn't understand what he felt just as Lensherr ends their discussion and leaves. Ten years later Kal-El's spaceship reaches Earth's solar system in the midst of a meteor shower that was left over from Krypton's destruction. Xavier and Irene Adler detect Kal-El's arrival, in which the latter refers to him as the "Child of the Star". Kal-El's vessel makes landfall in Smallville, Kansas where he is founded and adopted Jonathan and Martha Kent. Martha named the baby Clark.
Chapter 2: First EncounterYears later, a 19-year-old Clark Kent have been living in the Fortress of Solitude for four years, where he has been training in using his new-found powers powered by Earth's yellow sun, and as well learning his Kryptonian origins and civilization, and clad in a costume modeled after Krypton's defense military. He also catches interest in the "X-Gene" that grants people different powers along with other similar individuals that had been using their abilities for good. Meanwhile, while using Cerebro, Professor Xavier detects Clark's presence at the North Pole and mistakes him for a powerful mutant. He assembles Jean Grey, Cyclops, Storm, and Wolverine on his journey to meet Clark. The X-Men and Clark encounter on an amicable approach. Alarmingly for Xavier and Jean, they couldn't read Clark's mind. The X-Men are soon surprised of Clark's Kryptonian origins (in which Xavier realizes the dread feelings he sensed years ago was Krypton's destruction) and his intentions of using his powers for good. However, Xavier forewarns Clark that his actions would compromise the existence of mutants that has been kept secret and that humanity is not ready to accept those with abilities. Clark agrees and decide to help people discreetly. Xavier offers Clark to join the Xavier Institute for the cause of seeking peace and acting as shining examples to mutants and making the public to be not afraid of mutantkind; in which Clark readily accepts. Notes:
- Jor-El's message is based on the message that Jor-El gave Superman in the original Superman movie.
- The Avengers, Spider-Man, and the Fantastic Four are mentioned in several newspaper articles read by Clark.
Chapter 3: New to the NeighborhoodClark becomes a resident of the Xavier Institute and his heroics is eventually caught by the news, whom they dubbed him as "Superman". Unfortunately, his actions also caught the attentions of Magneto. Meanwhile, Kurt Wagner is recruited to the Institute and takes the identity of Nightcrawler.
Chapter 4: It's Just a PhaseSuperman and the X-Men seeks to recruit Kitty Pryde, who is developing mutant powers and also a big Superman fan. However, Lance Alvers, a troubled mutant who can create earthquakes, attempts to win over Kitty. Superman comes into blows with Wolverine's nemesis Sabretooth and prevails in defeating Alvers, who is shortly recruited by Mystique and adopts the name Avalanche.
Chapter 5: Gone RogueWhen Rogue accidentally triggers her mutant power, Superman and the X-Men, with help from Gambit, head off to recruit her. However, Mystique isn't willing to let her out of her sights to become one of them. However, Superman and the X-Men succeed in winning Rogue over and discovering Mystique's, and by extent Magneto's, involvement. It is also learned from Professor Xavier's colleague Hank McCoy that the reasons for Superman's Kryptonian biology absorbs massive solar energy which allows him to become immune to X-Gene powers, such as being allowing Rogue to touch Superman. Elsewhere, Mystique reports her failures to Magneto and more concerning on Superman's interference. She is met by Irene Adler, who reveals to her that Superman is part of a prophecy she foreseen since Superman's arrival to Earth that will have an impact on the planet; a prophecy that Magneto interprets as Superman being destined to lead mutantkind over humankind.
Chapter 6: FriendsSuperman meets the Avengers (Captain America, Thor, Wasp, and Giant Man) in Latveria and helps them in foiling an illegal weapons demonstration orchestrated by Doctor Doom. The Avengers greatly thanks Superman for his help and offers him membership into their team. But Superman kindly refuses. In gratitude, Captain America gives him a communicator to call the Avengers if he ever needs them in times of trouble. Soon after Superman arrives in time in rescuing Jean from Fred "Blob" Dukes. Captain America later visits Wolverine and recalling his encounter with Superman and his superior, Nick Fury, was not too thrill of Superman's decision of becoming an independent superhero.
Chapter 7: In a New York MinuteClark Kent goes to the Daily Bugle as part of his university study and meets New York's web-crawler, Spider-Man, who is currently tracking down a crime spree committed by the mutant speedster Quicksilver. With the X-Men's help (including their recent member Spyke) Superman and Spider-Man catches Quicksilver. Superman also brings the ire of the Kingpin, and the keen personal interests of Doctor Doom.
Chapter 8: Christmas with the X-MenClark spends the winter holidays at the Xavier Institute.
Chapter 9: Stuck in the Middleverse with YouSuperman meets the Fantastic Four for the first time and helps them in repairing International Space Station. The Four helps in return in rescuing Nightcrawler and the mutant Forge from the dimension pocket of the Middleverse. Thereafter, Professor Xavier brings revelation to Nightcrawler of being the biological son of Mystique.
Chapter 10: Training DaySuperman and the X-Men competes the Brotherhood on a two-day hiking trip. During this trip, Superman gains some gratitude from some members of the Brotherhood, with exception from Quicksilver who holds a envious grudge over the Man of Steel. Meanwhile Mystique infiltrates S.H.I.E.L.D. and frees Xavier's vengeful half-brother Cain Marko, The Juggernaut, in order to bargain his release in acquiring Cerebro. However, Juggernaut rejects her offer and pursue his relentless revenge on his half-brother. Superman, the X-Men, and the Brotherhood are forced to team-up against Juggernaut at the ravaged Institute. After defeating Juggernaut and turning him over to S.H.I.E.L.D., Nick Fury finally meets Superman and acknowledge his good intentions for the world, but is albeit warily of the Kryptonian who can fight on equal terms with Juggernaut. Regardless Fury appreciate Superman for what he is doing along with the X-Men and decide to remove any mention of him or the X-Men in his reports. Magneto is informed of the developments by Mystique and Quicksilver. He decide to make his move by using a deterrent against Superman that he discovered from Smallville: Kryptonite.
Chapter 11: FamilySuperman prepares his first Trans-Warp flight to Mars and Jupiter. Meanwhile, Wolverine goes into the Canadian wilderness to find Weapon X and is brainwashed by the doctor who gave him his adamantium skeleton. Shadowcat and Nightcrawler saves Wolverine along with Sabretooth from their mental conditioning, and destroying Weapon X in the process. The benefactor of Weapon X, Graydon Creed, scraps the project and decide to rely on less "organic means" for his anti-mutant agenda. Elsewhere in deep space, Brainiac detects Trans-Warp signature coming from the Solar System and makes its way there to finishing off the Last Son of Krypton.
Chapter 12 & 13: Fated HourMagneto puts his master plan into action to recruiting Superman to his cause as he does the same for Cyclops and his long lost brother Alex Masters. Upon fateful meeting, Magneto has long observed and verified Superman as the messianic "Child of the Star" from Irene Adler's prophecy supposed to lead the mutant race. However, Superman firmly rejects Magneto's proposition and his extreme ideals. Having expecting this, Magneto expose Superman to Kryptonite and imprison him on his sanctuary Asteroid M, and reveals his intentions of using Asteroid M as a giant conductor to amplify his magnetic powers in bringing forth a meteor shower to Earth, wiping out humankind and having the mutants to be safe on Asteroid M and exploit their dominance over whatever is left remaining on Earth. Magneto abducts the X-Men, and Gambit, to Asteroid M. But his plans is undermined by Avalanche, who is appalled by Magneto's genocidal intentions, informs Cyclops and Alex about this and freeing the X-Men and Superman. The heroes and Avalanche defeats the Brotherhood, but Magneto manages to pull enough meteors into Earth's orbit before making his escape as Asteroid M is falling apart. Superman uses all his powers in destroying every meteor and, with the combined assistance of Cyclops and Alex, incinerating Asteroid M. The Earth is saved and a reformed Avalanche and Gambit officially joins the X-Men.
Epilogue: Loose EndsMystique visits Irene Adler and tells her that her prophecy is incorrect concerning Magneto's failure in turning Superman to his side. But Adler state it is not, as the events on Asteroid M fulfilled the first part of the prophecy and that the prophecy is on track, but not yet completely fulfilled. Superman and the X-Men celebrate their recent victory at the Kent's farm. But Superman then notice that Magneto couldn't be alone or powerful enough to complete his plans. He makes contact with Earth's Sorcerer Supreme, Doctor Strange, who identifies magic were involved and traces to its bearer: Doctor Doom. Superman travels to Castle Doom in Doomstadt, Latveria, and finding Doom awaiting him. He explains to Superman that he aided Magneto for his own reasons and believe that there will be a war between humans and mutants. After Superman made his leave, Doom's adopted daughter, Anita LeRoux, shows some affections for the Kryptonian.
Book Two: Reckonings
Chapter 1: The ReturnThe Institute welcome new mutant students, dubbed as the New Mutants, and assigns Superman as their instructor. Trouble a brew when the Brotherhood (without Mystique nor Magneto's leadership) gatecrash Bayville High's girls' championship soccer match and threaten to expose mutantkind to the world. The X-Men and Superman stops the Brotherhood's rampage and exposing themselves in the process. Professor Xavier wipes every witness of their memory. The X-Men have mixed emotions regarding that humanity is not ready for mutants, but remains hopeful that people might tolerate mutants after witnessing some people showing awe and admiration of seeing Superman.
Chapter 2 & 3: Siryn's SongAnita LeRoux, known as Siryn, arrives in the United States and enrolls in Bayville High, becoming the de facto leader of the Brotherhood, and attempts to woo Superman with her magic and mutant powers of vocal suggestion. She proves herself trouble in interfering Superman's heroics and close to threatening the lives of the X-Men, until the Man of Steel builds a neutralizer which cancels out Siryn's voice. Though defeated, Siryn is not deterred as Doom reassures her that the days' events had goes as plan regarding to his associate's manipulations of certain humans under Nick Fury's S.H.I.E.L.D. will greatly benefit their cause in the end.
Chapter 4: From the AshesJean Grey loses control of her telepathic and telekinetic powers and abilities due to her alternate personality called the Phoenix.
Chapter 5: With Friends Like TheseBoom Boom flirts with Nightcrawler, and then gets a visit from her criminal father who wants her to commit a crime for him. After her father is arrested, Boom Boom believes she doesn't belong to the Institute and intends to leave until a talk with Superman convinced her to change her mind.
Chapter 6: BedazzledPop singer Alison Blaire visit Bayville on her music tour and is secretly a mutant. Clark Kent immediately recognizes Alison as her childhood friend.
Chapter 7: Fitting InAlison Blaire, also known as as "Dazzler", adjust to her enrollment in the Xavier Institute. Meanwhile, Siryn enlist the Black Cat in stealing a magical artifact called the Stone of Arkanas which could amplify her powers. In the end, Dazzler proves herself as an X-Man and defeats Siryn, and consequently becoming the latter's nemesis.
Chapter 8: Friends IndeedDuring an assigned interview for the Daily Bugle, Clark Kent is reacquainted with his childhood friend and powerful industrialist, Lex Luthor, who knows Clark is Superman (which Lex knew beforehand since witnessing his powers in action while living in Smallville) and as well as mutants from carefully analyzing the Brotherhood attack in Bayville High. Rather than seemingly to blackmail Clark, Lex helps him in rescuing Spider-Man from the Kingpin's clutches with Siryn surprisingly helping along as well. Meanwhile, the New Mutants and the younger X-Men throws a party at the Institute while Professor Xavier and his faculty are away to mend Juggernaut's stasis cell. Unknown to them, Rogue's friend "Risty", a disguised Mystique, infiltrate the Institute. Fortunately, Superman arrives in time and foiling Mystique's theft of the Institute's information on their students. Mystique is let go after claiming that she is doing this to protecting Nightcrawler. Xaiver meets with Nick Fury and learns from him that there is an undoubted possibility that S.H.I.E.L.D. is being infiltrated by anti-mutant elements which also were responsible for releasing Juggernaut. Xavier, Storm, and Wolverine soon returns to the Institute that is cleaned up from the previous night and gets a surprised visit from Lex, who offers an alliance between them should mutants inevitably be reveal to the public. The X-Men, initially reluctant, accepts Lex's offer after Clark vouches for him. As Lex returns to Lexcorp, he opens a computer file pertaining to the "Sentinel Project".
Chapter 9: Date NightClark goes on a date with Alison. However, Siryn and Quicksilver decide to ruin their day.
Chapter 10: Beast WithinDr. Hank McCoy has no energy left to fight his mutation, which forces him to be a violent Beast. Superman, the X-Men, and along with the Fantastic Four, tries to help McCoy while encountering the Friends of Humanity, an anti-mutant organization led by Graydon Creed, who also have set their sights on the doctor.
Chapter 11: HomeAlex Masters gets caught in a riptide while surfing using a surf board fitted with a webcam. Scott (who's visiting his brother) goes out to rescue him; however, the brothers are eventually stranded on an island that is being excavated by Doctor Doom and Siryn. The brothers are captured and are used to draw Superman's (with Jean and Storm) to Doom, who offers the Man of Steel a chance to return to Krypton through the magical powers of an Orb of Agamotto, which is the purpose for Doom's excavation. Superman, however, destroys the Orb and reveals to the stunned Doom and Siryn that Krypton has long been destroyed and he is the last of his kind. Doom and Siryn depart before warning Superman to abandoning his relationship with Alison Blaire. Superman accepts the fact that even though his home planet and birth parents are gone, he is fortunate to still have a family with the X-Men.
Chapter 12: AngelsDuring Christmas time, Warren Worthington, a winged mutant inspired by Superman's heroics, becomes an vigilante in which the public dubs him the "Angel". Magneto to frame him, in order to instill hatred against mankind, forcing Superman, Dazzler, Cyclops, and Jean Grey to set things right.
Chapter 13: Stormy WeatherWhile trying to discipline Spyke, Storm is tormented by the Hungan, an evil African shaman who wants to steal her power while working for a malevolent figure, along with the mercenary Deadpool as hired help. Superman and the X-Men are thankfully assisted by Storm's old flame, T'Challa, also known as the Black Panther. Though the Hungan is caught, his mind is put into a catatonic state by his former ally Mesmero to prevent him from revealing the shaman's ties to his true master: Apocalypse. With the failure to capture Storm to siphon her mutant powers, the followers of Apocalypse focus on other means in releasing their ancient mutant lord while growing concern of Irene Adler's "Star Child" prophecy that will prove problematic in the future. T'Challa helps Superman in return by showing him an ancient temple in Wakanda containing an advanced alien weapon recovered many centuries ago, in which Superman recognizes it as part of a Kryptonian spaceship. Meaning that the Kryptonians had visited Earth before.
Chapter 14: Night on the TownThe female X-Men, fed up with playing second fiddle, form a vigilante form a vigilante crime-fighting group called the Bayville Sirens. Their vigilantism provokes the Kingpin to hiring the assassin Bullseye and Deadpool (who is sore from his recent encounter with the X-Men) to eliminating the Sirens after targeting his smuggling operations. Luckily, Superman, Dazzler, and (reluctantly) Daredevil intervenes in subduing the hitmen, and the Sirens are convinced to disband. Meanwhile, Kingpin brings bad news of the foiled shipment to his buyer: Sebastian Shaw. However, Shaw is not upset by it as everything has gone as planned. The shipment of equipment supplied by Doctor Doom had been transferred to Graydon Creed's Friends of Humanity. Shaw also show some interests of Superman and Doom's schemes that might benefit for the Hellfire Club.
Chapter 15: War WoundsMagneto and his Acolytes steals equipment pertaining to Project Rebirth, the technology that gave the powers to super-soldier Captain America, and abducts its head researcher, Dr. Bruce Banner. Nick Fury recruits his old comrade Wolverine, Superman, and the X-Men along with the Avengers in destroying Rebirth and preventing Banner from turning into the Hulk. Magneto, however, uses Rebirth to de-age himself before it is destroyed and sets the Hulk on the heroes. Eventually the Hulk is subdued and calmed through Superman's equal strength and Charles Xavier's telepathy. Superman also reveals to the Avengers of his alien origins. Thor immediately realizes and reveals to Superman that Krypton's destruction and the death of its people did not went unheard for the people of Asgard.
Chapter 16: Strange ThingsMesmero kidnaps and brainwashes some of the X-Men into stealing the first key to Apocalypse's prison. After Superman helps Doctor Strange in saving his ex-wife Clea from Dormammu, Strange helps the Man of Steel and the X-Men in finding Mesmero, who is allied to the sorcerer's nemesis Baron Mordo. Despite defeating the villains and rescuing their teammates, the first key is already been taken. Doctor and Siryn later visits Irene Adler to talk over the prophecy; in which Adler advise them to take heed of the last phrases, and as well foreseeing that Superman will not be fighting alone to bring back something lost to Earth: justice.
Chapter 17: CrashdanceThe Bayville High Sadie Hawkins dance arrives, and everybody is scrambling for dates. Alison meets an unpleasant encounter with her ex-boyfriend, Shinobi Shaw. While this is going on, Forge constructs a device to lengthen Nightcrawler's teleportation reaches, however the creatures he encounters while passing through a 'separate dimension' during his teleport, manage to escape through open portals Nightcrawler leaves behind.
Chapter 18: Darkest KnightClark Kent and Peter Parker are sent to Gotham City to interview CEO of Wayne Enterprises, Bruce Wayne. The Kingpin also expands his criminal operation in the city which attracts the attention of the Batman. Clark soon learns of Wayne's dual identity and helps him along with Spider-Man teaming-up in stopping The Joker, who double-crosses the Kingpin, from poisoning Gotham with his Joker Gas. Meanwhile, Amanda Sefton, Taryn Fujioka, and Paul Andersen are invited to the Xavier Institute and learn in their friends' well kept secret.
Chapter 19 & 20: Fish StorySuperman is bring into resolving a near-international crisis as the Fortress of Solitude lies in the territory of King Namor of Atlantis. Cooler heads prevail through the Fantastic Four and Namor's cousins, Namorita and Arthur Curry, the latter of which is a familiar friend from Clark's childhood. After some heated words, mostly by Namor, the matter cools when Superman and Namor agrees on a truce in which each would protect the Fortress and Atlantis from their enemies. Furthermore, Superman learns the location of the missing Kryptonian ship to be transformed into a shrine in Atlantean waters. Meanwhile, the X-Men and New Mutants arrange a field trip to the wilderness with Beast. Unfortunately, hunters catch Beast, thinking him to be Bigfoot
Chapter 21 & 22: A Boy and his DogA month before Krypton's destruction, Superman's pet dog Krypto was on a Trans-Warp prototype test conducted by Jor-El and was lost in space. Decades later, Krypto's ship arrives on Earth and is reunited with Superman. Meanwhile, a community of mutants known as the Morlocks are being abducted by the Friends of Humanity to be use in their experiments; namely the creation of mutant-killing super-soldiers genetically bonded with Kryptonite. The X-Men along with Krypto and Spider-Man engage in their second encounter with the Friends of Humanity, and managing to beat their mutated soldiers. After saving the captured Morlocks, Spider-Man's secret identity is accidentally revealed to his allies but his secret is kept safe as Superman also reveals his much to Spider-Man's surprise. Dazzler suddenly manifest Kryptonian-like powers and it is soon learned that she is the direct descendant of a Kryptonian who was stranded in Earth's past.
Chapter 23: HexedSiryn frees a mentally unstable, but immensely powerful mutant named Wanda Maximoff, and makes her a member of the Brotherhood much to the horror of her brother Quicksilver, as a decisive advantage against Superman and the X-Men. Superman's presence on Earth garners the notice of Thanagar, whom dispatch Lieutenant Colonel Shayera Hol to offer Superman sanctuary on her home planet. But Superman declines her offer and she and Superman helps the X-Men in beating the Brotherhood. Shayera decides to stay on Earth to study its culture and, influenced by Shadowcat's suggestion, adopts the name Hawkgirl. Wanda is revealed to Siryn's manipulations and angrily leaves the Brotherhood, and is then taken under the guidance of Agatha Harkness. Mystique has an emotional reunion with her children.
Chapter 24: Space CaseBrainiac Mark V finally arrives in Earth's orbit, but crash land on the moon. S.H.I.E.L.D. alerts Superman and the X-Men about the Brainiac module and travel to the moon to capture and destroy it. There they meet the Inhumans and subsequently finds the Mark V, but it is reveal to have developed sentience and independence from Brainiac's orders. Although wary at first, Mark V, shorten as "Mark", proves himself in helping the heroes and the Inhumans in stopping the Friends of Humanity from stealing the Terrigen Mist which grants the Inhumans their powers. Mark is adopted to the Institute.
Chapter 25: The First HurrahAfter Clark finish his internship at the Daily Bugle, he is brought to a reunion with friends from Smallville: Oliver Queen, Wally West, Victor Stone, Arthur Curry, and Lex Luthor.
Chapter 26: AccusedKree Supreme Public Accuser Ronan learns of the last Kryptonian Superman is living on Earth and sets out to place him on trial for "crimes" against the Kree Empire by abducting the X-Men and accusing them for harboring the Man of Steel. Superman's rescue of his adopted family is assisted by Earth's Green Lantern John Stewart. Upon arriving at the trumped up trial, Superman allows a right of Appeal by Combat - in which he faces Ronan in single combat. The trial ends when the Kree Supreme Intelligence favors Superman due to him saving a Kree citizen and disappointed by Ronan's unbecoming behavior, and pardons him and the X-Men, as the Kree Empire's quarrel with Krypton is ended since the planet was destroyed.
Chapter 27, 28 & 29: Zero HourWhen clashing with Sabretooth, Wolverine and Sabretooth are captured by the Friends of Humanity and tested for Bolivar Trask's Sentinels. It is also discovered that Graydon Creed is the son of Sabretooth and Mystique. Wanda, accompanied by Agatha Harkness, and Lex Luthor visit the Institute and warning Superman and the X-Men of an upcoming battle with Magneto and his ally Doctor Doom; in which Lex provides them evidence of the Sentinel Project, which was commissioned and shelved by S.H.I.E.L.D., and were the illegal shipments sent to the F.O.H. by Doom and Sebastian Shaw. Superman, the X-Men, along with Wanda confronts and battle Doom, Magneto and his Acolytes. This, however, part of Doom's and Magneto's plan in which the F.O.H. sends their Sentinels to combating Superman and the X-Men, and exposing their existence to the public, while the F.O.H. attacks the Institute and kidnapping Professor Xavier. Joined by Mystique who arrives too late to warning them of the F.O.H., the X-Men manage to evacuate the New Mutants with surprising help from their past allies: Aquaman, Flash, Green Lantern, and Hawkgirl. Although the Institute is destroyed in the process, forcing everyone to hold out in the Fortress of Solitude. There, Superman contacts further reinforcements from Batman, Spider-Man, The Avengers, The Fantastic Four, and Thor's acquaintance Diana, the Amazon princess of Themiscyra. Jean resort to making contact with the Phoenix in order to finding Xavier. The two surprisingly made peace when the spirit of her deceased childhood friend Annie intervene, allowing Jean to locate Xavier to be in the former site of Area 51, a disused S.H.I.E.L.D. facility being used by the F.O.H. as a launching point for their Sentinels. The heroes convened on Area 51, freeing Xavier, Wolverine, Sabretooth, and another prisoner, the Martian J'onn J'onzz. A desperate Graydon Creed launch his surviving Sentinels to attacking Genosha. Superman, Hawkgirl and Green Lantern destroys the Sentinels before they could make landfall on the island. The trio finds Magneto and Doom, who expected their heroic efforts to happened to bear witness by every mutant on Genosha to furthering the prophecy. But to the villains' shock, Superman subverts his "destiny" by telling everyone to following their own destiny. The moment is interrupted by the sudden arrival of the Brainiac Module Mark VI, which assimilates the fallen Sentinels and beginning its objective of destroying Earth. Problems exacerbate by panics spreading in the United States and an escaped Juggernaut. The Fantastic Four, Avengers, and Spider-Man deals with the panic while the X-Men heads to stop Juggernaut while Xavier goes to a congressional hearing to placating the public's fear of mutants. The remaining heroes Batman, Wonder Woman, Flash, Aquaman, and J'onn joins Superman, Hawkgirl, and Green Lantern in stopping the Mark VI which comes to its end when its brethren Mark V infects it with a computer virus. The seven heroes then joins the X-Men in finally defeating the Juggernaut.
Epilogue: Public RelationsWith Superman and the mutants revealed to the world, the Man of Steel agrees to an exclusive interview for the Daily Bugle, in which he reveals his alien origins, his relationship with the X-Men, and the newly formed Justice League. He assures the public that people don't need to be afraid of him, or mutants, and that the Justice League is not there to conquer them, but only to provide an example, and it's up to them to follow it. At the Brotherhood of Bayville Boarding House, Fred and Todd sit on the rooftop to watch the sunset and give a toast with their sodas to the Justice League. In New York, Wilson Fisk sees the League as a unbecoming threat to his operations and realizing the need to have deterrents against the heroes; thus getting rid of Superman and his League becomes a top priority. In Latveria, Doom quietly contemplates Irene Adler's prophecy that had finally foretold the League's creation. He breaks out of his silence by Siryn and states that the League changes nothing in the end. At the Academy of Tomorrow, Sebastian Shaw, his son Shinobi, Emma Frost and her Hellions have their own silent opinions on Superman's speech and its impact on the Hellfire Club. Sebastian sees that the coming year will be interesting. Somewhere at an undisclosed location, Graydon Creed is completely outraged to learn about Superman's alien origins. He gives an order to the F.O.H. to eliminate Superman and the League no matter the cost; however, Creed realized that with Trask arrested, the F.O.H. is severely underfunded. He then suddenly receive a phone call from a woman who shares similar reasons against the League and identifies herself as Madame Hydra.
Book Three: Changes
Chapter 1: New Beginnings
Chapter 2: School Daze
Chapter 3: Keep Your Enemies Closer
Chapter 4: The Price of Fame
Chapter 5: Polarity
Chapter 6: You Can't Go Home Again
Chapter 7: Testing Mettle
Chapter 8 & 9: Behind Enemy Lines
Chapter 10: Punishment
Chapter 11: Shredding Spykes
Chapter 12 & 13: Deep Trouble
Chapter 14 & 15: Saturday at the MuseumNotes:
- Adaptation of the Justice League Unlimited episode "Hawk and Dove".
Chapter 16: Good IntentionsNotes:
- The opening of Green Arrow's bust is similar to the very first episode of Justice League Unlimited "Initiation".
Chapter 17: Matters of State
Chapter 18: Tidings of Comfort and JoyNotes:
- Adaptation of the Justice League episode "Comfort and Joy".
Chapter 19: Worlds of WarNotes:
- Adaptation of the Justice League episode "War World" and the two-part Superman: The Animated Series episode "The Main Man".
Chapter 20: Tangled Webs
Chapter 21 & 22: Best of Enemies
- Adaptation of the Justice League episode "Maid of Honor".
- Lex Luthor makes a sarcasm of having a henchman named Otis, who is Luthor's henchman in Superman: The Movie in which this was not went unnoticed by Deadpool.
Chapter 23: Family Matters
Chapter 24: Lost and Found
Chapter 25: The Sins of the Mother
Chapter 26: Night Stalkers
Chapter 27: The Last Laugh
Chapter 28: Heirs
Chapter 29: Rumble in the Jungle
Chapter 30: Coup d'Etat
Chapter 31: Myxed UpNotes:
- An adaptation of the Superman: The Animated Series episode "Mxyzpixilated".
Chapter 32 & 33: Identity CrisisNotes:
- An adaptation of the Superman: The Animated Series episode of the same name, and the Justice League Unlimited episode "For the Man Who Has Everything" (itself based on the Alan Moore story of the same name).
- The end of Superman and Doom's fight is similar to the 2003 Daredevil movie, in which the Kingpin discovered Daredevil's identity, but wouldn't be able to use it against him without admitting he got beaten by a blind man.
Chapter 34: Phantoms
Chapter 35: Flashpoint
Chapter 36, 37, & 38: The Search for Sentrius
Chapter 39: Battlefield: Earth
Chapter 40, 41, &42: When Heroes Fall
Epilogue: Brand New World
Book Four: Destinies
Chapter 1: Darkened Horizons
Chapter 2: Shadows of the PastNotes:
- Adaptation of Superman: Earth One.
Chapter 3: Aliens in the Backyard
Chapter 4: For We Are One
Chapter 5 & 6: Revolution X
Chapter 7: Apokolips Now!Notes:
- Adaptation of the Superman: The Animated Series episode "Legacy".
Chapter 8: Dark Infection
Chapter 9: Iron SupplementsNotes:
- Adaptation of the Iron Man films
- The B.A.T. and Batman's gadgets are references to the Batman: Arkham Series.