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- "A few weeks after the Jewelbilee, what was supposed to be a proud day that commemorated Auradon's glory turned into a massacre the moment Kirito freed Zevon from the Isle of the Lost and recruited him into his rogue army that we now call the Shadowkeepers, who killed all of the civilians and corrupted Mal with the Darkness. But, what traumatized us the most wasn't her betrayal or the deaths of her friends, but Zavala's death, and now, what we saw proved to us that no one is safe. Not anymore."
- — Ikora Rey highlighting the start of the Shadowkeepers Apocalypse
The Shadowkeeper Apocalypse (also known as the Second Collapse) was a massively cataclysmic system-wide conflict fought between millions of Guardians and inhabitants of the Solar System and Kirito and Asuna and their armies of Shadowkeepers, Shadow Army and Supplicants minions, and Ghosts of Nagasaki to take back Auradon, save Mallory Bertha, and protect the Light. Although this crisis was initially triggered when Mal killed Maleficent, it actually began when the Shadowkeepers murdered countless people in Auradon, including Ben, Evie, Suguha Kirigaya, Emperor Calus, the Auradonian Kids' parents, and Commander Zavala, in order to take over all of Auradon and begin an eight-year reign beyond the heart of Aincrad. Unlike the previous enemies the Guardians killed, the Shadowkeepers sought to rewrite history and create a dark future, with them controlling all worlds as gods.
Prelude: The Swordsman's Arrival
- "The Dragon’s Eye has awakened. It is on a little world. A human world. They would only wield its power… But our allies know its workings as they never will. They are ready to lead. And our forces will follow. The world will be theirs. The universe yours. And the humans, what can they do but burn?"
- — An unnamed Taken commander, speaking to the Darkness about Kirito and Asuna.
Some time after the Guardians' victory of the Dimensional Wars, the Darkness, having found a still-open portal, sent the Pyramids into the dimensional gateway to recruit its new allies: Kirito and Asuna. Having known firsthand about how they had seen what it saw and mourned for the deaths of their friends and of innocence, the Darkness not only gave them back their powers from Sword Art Online, but also granted them permanent access to its Pyramids, knowing that they can succeed where its previous forces failed.
Upon accepting the Darkness's gift, after stepping out of their dimension and into the Guardian's universe, Kirito and Asuna recruited both the Shadowkeepers and the enemies of Light, instilling into them a profound sense of freedom and purpose, promising them that they would be the one to save them and those cast out and left for dead by their own people from the Traveler's lies.
Attack on Auradon
- "I'm so sorry. I'm sorry, I just... I thought that... I was afraid to tell you. I thought I was gonna lose my life. But I had to do something! I had to protect my birthright! It's just... I wish things could've been different."
- — Mal, talking to Petra Venj shortly before leaving with the Shadowkeepers.
Some weeks after the Jewel-bilee, the Shadowkeepers and their newly-assembled Shadow Army freed the son of Yzma known as Zevon from the frozen prison on the Isle of the Lost before launching a high-stakes invasion on Auradon that resulted in Mal's corruption at the hands of the Darkness and the deaths of countless civilians and heroes, including Zavala. Kirito and Asuna, having triumphed over the now-dead Zavala, proceeded to launch the codes for the Darkness's corruptive-matter system, simply known as Lightfall, which summoned waves of malevolent Blights that destroyed everything that Auradon stood for, killed all living beings of Light and civilians of Auradonian blood within it, and turned the entire city into a realm of Kirito and Asuna's ideal birth worlds. Although the fall of Auradon itself was unfathomable and the exact aftereffects of this event were unknown, it is certain that Petra Venj was the only survivor.
A New Aincrad
- "For years, the world had been bound by aspects of a failed past, full of lies that the Traveler brought upon this universe. But, we knew the truth. In Light, there was only weakness. Only failure. Only subjugation. Only death. But where the Light took, the Dark gives. No longer will we be pawns of the Light's lies. No longer will we stand by and let those monsters and so-called heroes abuse our people. No longer will we watch the lives of those we care for be lost. In Darkness, there is only strength. Only power. Only victory. Only freedom. Only life. And we shall rise forever!"
- — Kirito, rallying the forces of Darkness.
Moments after taking over Auradon, Kirito and Asuna set up countless programs and SIVA networks from his computer that the Pyramids used to rebuild Aincrad as they saw fit and split up the Shadow Army into its six respective groups: the House of Shadows, led by Kotrik, Bloodcrafter of Kirito, a notorious Fallen Kell of Shadows who stole Guardian tech from The Last City; the Shadow Swarm, led by Zharves, Shadowcaster of Kirito, a surviving Hive Deathsinger who formerly served Crota and his father; the Shadow Divisive, led by Hydrax, Mindkiller of Kirito, a massive Vex Axis Mind Hydra who possessed the ability to stop time; the Shadow Legion, led by Gha'arn, Crownforger of Kirito, a powerful Cabal warlord who helped murder Calus and overthrow the Leviathan; the Reborn, led by Thu'urg, Blightmaker of Kirito, a Taken Cabal commander who helped ignite a new Taken War; and the Cult of Shadows, led by Vayeriks, Fatesmith of Kirito, Fikrul's right hand and a commander of the first Scorn.
Hoping to further weaken the Traveler, they sent their forces across the system to launch countless waves of devastating attacks against its forces, some of which led to the extinction of numerous human civilizations and permanent deaths of the heroes of those extinct worlds. Enraged by the atrocities committed by Kirito and Asuna, Ikora Rey and Rasputin, along with numerous Guardians hellbent on getting their revenge on the Shadowkeepers for killing Zavala, created Dawnrise Protocol in the hopes of fighting back against the Darkness and saving the Last City, while factions such as the Stygian Brood and the House of Lions would lead countless assaults against the Shadow Army and those who pledged loyalty to Kirito and Asuna.
- "Long before the Traveler came, I made a promise to live on for the sake of my friends and Fairy Tail. Now, it has called on me to speak on its behalf and help you fight back against the Black Swordsman and the Lightning Flash."
- — Lucy Heartfilia, speaking to the Guardian moments after becoming the new Speaker.
Some time after Dawnrise Protocol's initiation, Ikora Rey appointed Shiro-4 as the Hunter Vanguard and Luther Hargreeves as the new Vanguard Commander representing the Titans, while the Consensus would appoint Glynda Goodwitch as the Huntress Vanguard, Kakashi Hatake as the Shinobi Vanguard, Jotaro Kujo as the Meister Vanguard, and Lucy Heartfilia as the new Speaker in order to strengthen the defenses of the City and provide more protection for the Traveler.
- "Mayday! Mayday! Do you copy! Vanguard access code 0306! Guardian, requesting backup! I repeat! We need backup down here!"
- — Nova, Herrscher of Sumeragi, sending a distress signal to the Guardian approaching the Cosmodrome.
Due to the havoc caused by the Shadow Army, Sumeragi, led by Nova, Herrscher of Sumeragi and Skalos's son Sakodis, Heir to the Shadows, have reemerged from their hiding places, seeking to restore order and balance to the system. However, despite their strength and wit, Sumeragi's forces weren't enough to stop the Shadow Army. After a close encounter with Kirito and Asuna, Sumeragi retreated back to their base, but not before sending a distress signal aboard the Cosmodrome, initially beginning a truce with the Guardians.
The Cosmodrome Breach
- "My name is Kotrik. I claim the title of Kell of Kells for myself. The Given shall fall. The Great Machine will be reclaimed. To arms, brothers! Let us advance the work of Kirito, who has given us this strength!"
- — Kotrik, Bloodcrafter of Kirito, rallying his Fallen brethren shortly before triggering an assault against the Guardian.
Shortly after claiming the power of Fusion in the form of its subclass and arriving at the Cosmodrome, as the Guardian rendezvoused with Cayde-6 and Petra, they received a distress signal from Nova, Herrscher of Sumeragi, who warned them about the threat Kirito and Asuna posed to Humanity. Upon hearing from him, the Guardian investigated the impending source of the Shadows' emergence, fighting the House of Devils along the way, and arrived at the base, where they acquired the Ace of Spades, Thunderlord, and Gjallarhorn shortly before encountering Kotrik, who wielded a corrupted version of the Thunderlord and declared his intention to eliminate the forces of Light and carry out Kirito's mission to bring the Traveler under the influence of the Darkness before unleashing his Fallen army upon them. The Guardian barely escaped just as more Fallen Shadows overwhelmed the base.
Discovery of the Shadows
- "I was right... I was right all along... The day we've been dreading has finally arrived. The Black Swordsman is here."
- — Eris Morn.
Some time after the Guardian uncovered the source of the Shadows' emergence in the Cosmodrome, Eris Morn, aided by her new recruit Anna Blue, intercepted a distress signal coming from the Hellmouth, searching for answers on Luna. After traversing deeper within the Scarlet Keep, she stumbled upon an abandoned Clovis Bray facility and touched a black surface, which revealed itself as some kind of footage. Upon getting a closer look at it, she discovers what happened to Mal back when she was a child and that the two adult Warlocks shielding her from Maleficent's attacks were her parents Kaguya Narusaka and Hendrick Yor.
A Nightmare's Return
- "The overall objective of this is to save a certain high-value person - Mallory Bertha. She has been corrupted by the Darkness and made the Dragon Queen of Auradon and the Isle of the Lost. She must be saved from the Darkness. But we will have to defeat Kirito’s armies of Shadows in order to accomplish this."
- — Luther Hargreeves.
- "You are too late. The world now knows the truth about Mal. And soon, everything they once thought existed will be forgotten. This is your end. Accept it."
- — Kirito, A Forgotten Interference.
Scourge of the Insurrection
- "Welcome to the end of the world. The dark future created by the Shadowkeepers. The universe corrupted by a power they don't understand."
- — Praedyth.
Fighting Kirito for the First Time
- "You claim to be a defender of humanity, Guardian. But, in the end, you’re just a person… someone who will always fall into the dark. No matter how fast you run, how far you go, and how hard you try to fight, it will catch up with you. The Light thought it could make you soft and sensible, but you have yet to feel all the pain I felt when I lost my friends and family! And this time, the Traveler will die for Auradon’s sins!"
- — Kirito, engaging the Guardian.
Allying with Sinon
- "I wished to become stronger by going beyond this sadness. But then, the Darkness came to our world and corrupted my friends. The Kirito and Asuna I knew were still heroes when they died... or left my world. If we work together, we can protect their legacies from those monsters who stole their names and memories."
- — Sinon.
- "Moments after Calus's death, the Red Legion massacred all the civilians of the Tri-State Area and turned Danville into a world without Light... an empire ruled by Dominus Ghaul with an iron fist. At the same time, the Shadow Legion have approached our world, seeking to carry out the Shadow King's mission. We must stop them before it's too late."
- — Valus Nohr.
- "We thought the Taken King's death crippled his armies. We were wrong. All it did was give them more power. The Black Swordsman is a monster, and he must die. For our sakes."
- — Viznoor, the Black.
The Hunt Begins Again
- "The story's true... Uldren and the Barons have returned... and this time, with an army. I've seen firsthand what they did to my people. Don't let them do the same to yours, Guardian."
- — Petra Venj.
- "I don't know much about what happened back then, but I do know that you can help me bring an end to the bloodshed, Guardian."
- — Felwinter.