Superheroes and mysteries go together like chocolate and peanut butter. The X-Men have proved this many times. While the team isn't known for fighting enemies who weave tangled webs of mystery, they have found themselves enmeshed in many conundrums involving members of the team. Members of the X-Men can't help but fall into wells of intrigue.
Over the years, readers have experienced these mysteries right alongside the team. Sometimes, fans learned the answers when the X-Men did. Other times, readers knew the answers and got to see what happened when the team found out, watching as secrets were revealed.
10 The Twelve
The X-Men ruled the sales roost throughout the '90s. It also saw writers of the books try to do something that former X-Men writer Chris Claremont did all the time - build long term plots that would hook readers and keep them following along.
One of these was the mystery of the Twelve. For years, fans tried to figure out exactly what the Twelve were and what role they'd play. They wouldn't find out until 1999, when it was revealed that they were mutants that when brought together could make someone a god. Apocalypse tried to use them for this purpose, but failed.
9 Mister Sinister's Moira Machine
Everyone knew that trusting Mister Sinister was a mistake, but they didn't really have a choice. The mutant nation of Krakoa was open to all mutants, and Sinister had something that they needed - the largest genome library on Earth, which contained basically every living mutant. Sinister was made a member of the Quiet Council, the island's government, and everyone kept a watch on him.
However, they didn't keep a good enough watch. Sinister found out the greatest secret of the island nation - that Moira MacTaggert was a mutant - and built his Moira Machine, which allowed him to reset the timeline. These "save states" wreaked havoc on Destiny's powers, making Sinister a wild card, and allowed him to push them all into the Sins of Sinister alternate timeline.
8 Sabretooth's Master Plan
In Wolverine (Vol. 2) #90, by writer Larry Hama and artist Adam Kubert, Wolverine tried to kill Sabretooth by popping one of his claws through the feral mutant's brain. It didn't work - Sabretooth's healing factor saved him - but he was reduced to a more animalistic state. Wolverine thought he was tricking everyone, and started living outside the mansion, while Sabretooth was kept in the Danger Room, lulled by its projections.
Boom Boom bonded with him, thinking him to just be a big kitten. There were moments when it seemed like he was tricking everyone, but they were gone just as fast. The truth would be revealed when he tried to kill Boom Boom, telling her that he had been playing everyone. Psylocke stopped him from killing Boom Boom, but almost died herself from wounds inflicted by Sabretooth.
7 The Mystery Of Bastion
Bastion appeared out of nowhere, in charge of Operation: Zero Tolerance, a secret arm of the US government. Activated after the Onslaught affair, O:ZT was given custody of Charles Xavier, and soon captured Jubilee. Bastion acted very familiar with his prisoners, yet no one really knew anything about him. O:ZT made their grand attack on the X-Men, but were rebuffed.
Bastion's secret wouldn't be revealed right away, making fans wait a little longer after Operation: Zero Tolerance. It was later discovered that Bastion was Nimrod, the ultimate Sentinel, who chased the X-Men through the Siege Perilous years before. The trip changed him from a robot to a cyborg, and he'd continue his attacks against the X-Men.
6 Nightcrawler's Parentage
Orphaned at an early age, Nightcrawler's parents were a huge mystery that he spent years trying to crack. Eventually, he and Rogue discovered his mother - Mystique. She had abandoned him shortly after birth, as her shapeshifting powers slipped and the villagers believed mother and child were demons.
His father's identity was a secret for years, but eventually it was revealed to be the mutant Azazel, which where Nightcrawler's demonic looks came from. While the story that revealed his identity, "The Draco," isn't well thought of, this mystery was long a foundational one in X-Men history.
5 Colossus's Possession
Colossus is a physical powerhouse, long anchoring the X-Men against the deadliest threats. He lived a violent life, yet he had the heart of an artist. Upon the establishment of the mutant nation of Krakoa, Colossus decided to live a quiet life farming and painting. However, his brother Mikhail, commanding Russia's response to Krakoa, was able to take control of him using a mutant known as Chronicler.
Chronicler's powers allow him to write the lives of people, making them do what he writes. Colossus became a member of the Quiet Council, and is a mole for Mikhail. He can't control his actions and only watches in horror as his life is suborned. This mystery is ongoing, as Colossus tries in vain to get someone to realize how far he's fallen.
4 The X-Traitor
Bishop was a member of the future X.S.E. organization. He came back in time chasing the criminal Trevor Fitzroy, but before he left the future, he met the elderly Gambit. Gambit told him the story of the death of the X-Men, showing him a recording that Jean Grey had made about a traitor on the team. For years, fans wondered about who would try to betray the team.
When Onslaught revealed himself as Professor X, the truth was laid bare. During his mindwipe of Magneto, a piece of the Master of Magnetism's evil planted itself in Xavier. This became Onslaught, a tremendously powerful psychic parasite that almost destroyed the X-Men and the world.
3 The Truth About Gambit
Gambit joined the team after helping a de-aged Storm. He was a man of mystery, playing his cards close to the vest. Everyone knew he had a secret, but no one knew what it was. As time went on, that secret would become less and less important, but eventually it started to eat away at Gambit. It drove a wedge between him and the team, made worse by Rogue and Joseph, a Magneto clone, starting a relationship.
Eventually, the team was captured by Erik the Red and Gambit was put on trial. Erik the Red, who was actually Magneto in disguise, revealed the terrible truth about Gambit. He was hired by Mister Sinister to guide the Marauders into the Morlock tunnels. The slaughter was too much for him to stomach, and he was only able to save one Morlock as he escaped.
2 Moira MacTaggert's Importance To Krakoa
Inferno was Jonathan Hickman's last X-Men story, and he went out by revealing the biggest secret of Krakoa. Readers had known all along about Moira's place in the Krakoan scheme of things, but the resident of the island had no idea about her being or a mutant or that she was even alive. That all changed because of two things.
The first was Mystique resurrecting Destiny on her own and the second was Xavier and Magneto revealing Moira's secret to Emma Frost. Emma told Mystique and Destiny, and they went after her. They only spared her, depowering her instead of killing her because of Doug Ramsey, but afterward everyone knew her secret.
1 Wolverine's Origin
Logan had little to no memory of his life before being found in the wilderness by James and Heather Hudson. Little by little, he learned the truth. Wolverine received his adamantium and memory problems from Weapon X, a super-soldier program. He'd soon start remembering things that happened decades in the past.
After Scarlet Witch depowered the mutant race, Wolverine finally got his memory back. He remembered his childhood in 19th century Canada, his dead Japanese wife Itsu, and so much more. Of course, the mystery is still unfolding, but many of the big parts have been revealed.