The X-Men have been rocked by a number of dark secrets over the years that have threatened to tear the team apart and destroy their foundations.

Marvel’s mutants are preparing for The Sins of Sinister event that will alter reality into a dark new world created by Mr. Sinister. The X-Men villain has found a new path working alongside the mutants in the Krakoan era. However, his “sinister secrets” have continued to destabilize the developing mutant nation in a few subtle ways.

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Of course, Mr. Sinister isn’t the only mutant who has kept dark secrets over the years. The X-Men were built upon a number of troublesome secrets that have defined characters and altered the status quo over the years. Characters like Gambit and Professor X have hidden secrets that blew the past of the X-Men wide open, and they weren’t alone.

One of the biggest changes in the X-Men's Krakoan era was the formation of a brand-new mutant island nation. The island not only provided a safe space to thrive, but it also gave the X-Men the chance to bring back fallen mutants using the Resurrection Protocols.

These protocols were kept secret from the rest of the world, as the prospect of immortality could have painted a further target on the island of Krakoa. Daily Bugle reporter Ben Urich uncovered the X-Men’s dark secret. Synch erased the knowledge from his memory, but Cyclops still decided Urich could reveal the secret of mutant immortality to the world.

Kurt Wagner had to deal with a few tragic revelations about his birth that continued to shock the teleporting mutant known as Nightcrawler. The revelation that his mother was the shape-changing mutant named Mystique was hard enough to accept. The fact that she abandoned him to die further traumatized Nightcrawler.

However, he would later learn an even darker secret about his birth. A powerful demon named Azazel revealed himself as Nightcrawler’s real father. He had sired a few different mutants over the years. They were all mutants with a connection to another dimension. Azazel hoped to use Nightcrawler and his siblings to help him escape from the Brimstone Dimension, but his plan failed.

Cable was the first to organize other mutants into a militaristic strike team known as X-Force. However, his father also took it upon himself to secretly form his own roster of X-Force after the Messiah Complex event. Knowing he needed to take a harder stand in order to prevent the extinction of the mutant race, Cyclops asked Wolverine to reform X-Force in secret.

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The team proactively took out threats to mutantkind using extreme methods. This didn’t sit well with other members of the X-Men when they discovered the truth about X-Force, and Cyclops ultimately decided to disband the team. However, Wolverine formed his own roster of the team and hid them deeper underground.

The threat of Onslaught plagued the X-Men for months before the evil psionic villain finally made his debut. The merger of Professor Xaver and Magneto’s troubled psyches created one of the X-Men's deadliest '90s villains, though his true identity was kept secret. He mentally confronted Jean Grey in an effort to cast doubt on her relationship with the X-Men’s mentor.

Onslaught took her deep inside Professor Xavier’s mind to uncover a secret he had kept hidden for years. Xavier had been secretly harboring an unrequited love for his young student that could have tainted their close relationship. She was able to ignore it as a manipulation of Onslaught, though the dark secret still led Jean Grey to question her relationship with Xavier.

Ultimate Marvel was quite different from the 616 universe. The stories updated characters like Spider-Man and the X-Men and their modern adventures were free of established continuity. The X-Men dealt with an ongoing threat of prejudice like their mainstream counterparts. However, they learned of a dark secret during the Ultimatum event that changed everything.

Nick Fury revealed to Magneto that mutantkind wasn’t the next evolutionary step for humanity. In the Ultimate universe, the mutant gene was actually created through genetic experiments that began in WWII. James Howlett/Wolverine was a soldier taken by Weapon X who was transformed into Mutant Zero before the new mutant gene accidentally spread across the world.

The X-Men trained in the use of their powers and abilities in what became affectionately known as the Danger Room. It was originally a mechanical workout room filled with traps and weaponry that tested their developing skills. The Danger Room was continually improved over the years with advanced alien technology that allowed it to create powerful hard-light holograms.

However, those alien advancements resulted in an unforeseen development. The Danger Room became self-aware and revealed itself to Professor X. He quieted its developing sentience and hid the evidence so the X-Men could continue to train. It eventually freed its mind and became Marvel's powerful robot known as Danger, which exposed Professor X’s dark secret.

The X-Men experienced a huge change in their status quo when the Inhumans released the Terrigen Mists into the atmosphere. A new wave of global Terrigen transformations began, though it also had a secondary effect that negatively impacted mutantkind. A fatal disease known as M-Pox began afflicting mutants who came in contact with the Terrigen Mists.

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Cyclops was one of the first to fall to the M-Pox, though the truth behind his death was kept secret. Emma Frost instead hid this information and allowed the X-Men to think Cyclops had died in battle with Black Bolt. This set the X-Men against the Inhumans in a nearly fatal war. It only ended when the X-Men learned the truth about Cyclops' death.

Mr. Sinister has always kept a number of important secrets close to his vest, though he occasionally teased the X-Men with them. During a discussion with Scott Summers/Cyclops, Mr. Sinister let it slip that there might be another Summers brother besides Alex Summers/Havok. This dark secret was eventually uncovered, though the layered reveal shocked fans.

Gabriel Summers/Vulcan was the younger brother of Cyclops and Havok, though he wasn’t the only one. Adam-X the X-Treme was also revealed to be a long-lost sibling in the powerful Summers family. He was genetically engineered using Shi'ar Emperor D’Ken and Katherine Summers’ DNA. Adam-X’s true lineage remained a poorly-kept secret for over 20 years before it was confirmed.

One of the most evil things Mr. Sinister ever did became a dark moment in the X-Men’s history known as the “Mutant Massacre.” His team of mutant killers known as the Marauders entered the sewers underneath New York City and began exterminating the mutants known as Morlocks. They were physically mutated which led them to hide away from humanity in their own community.

The X-Men learned the shocking truth that Gambit had played a role in leading the Marauders underground to the Morlocks. While he didn’t know they were going down there to kill the Morlocks, it was a harsh blow to the X-Men that damaged their relationship with Remy LeBeau. Gambit’s long history and debt to Mr. Sinister continued to haunt the X-Man for years.

Everything changed for the X-Men after they discovered Professor X’s darkest secret in X-Men: Deadly Genesis. The return of Gabriel Summers/Vulcan shined a light on a hidden chapter of the X-Men. His dark secret tainted the events of Giant-Size X-Men #1 which introduced a popular new version of the team as well as Krakoa.

When Krakoa captured the original team, Professor X gathered a new untrained squad led by Gabriel Summers to save them. They died in battle, and Professor X decided to cover up their sacrifice. He mindwiped Cyclops so he forgot his brother and hid the deaths of the students. The X-Men turned their backs on their former mentor when they discovered the dark truth.

NEXT: 5 Mutants Who Were Supposed To Save The X-Men (And 5 Who Nearly Doomed Them)

Entertainment reporter, writer, and all-around geek, Scoot Allan has written for print and online media sources like Geek Magazine, GeekExchange, GrizzlyBomb, WhatCulture, RoguePlanet.tv and the Urban 30 before joining CBR as a senior writer. He enjoys salad but prefers french fries.

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