The MCU is full of duplicitous characters pretending to be something they're not. It's not just the villains, although they really tend to be the most treacherous of all. But that is completely expected of them, and their deceit doesn't really come as a surprise. Some characters walk a fine line between light and dark, acting in amoral ways but never really going overboard.
The most unexpected and painful deceptions, however, come from the least expected sources. Sometimes heroes have to pretend too, whether for the sake of others or because they just don't have the strength to deal with the fallout. Whatever the reason, when the truth comes out, the consequences can be severe, and not even their superpowers can save them from facing up to their mistakes.
Clint Turns His Back On The Avengers
Grief makes people do crazy things. Everyone has different ways of processing it and some choose a darker path to release their anger and frustration. After his family disappears during the Snap, Clint goes down a path of rage and revenge, assuming his Ronin identity and basically becoming a serial killer.
Sure, he only kills bad guys, but Ronin's rage is just a projection of his own self-destructiveness. Clint is obviously chasing death, taking on increasingly more violent and reckless missions, and abandoning all his previous connections to the Avengers at a time when he should've been there for them.
Ultron Uses Wanda & Pietro
When the twins Wanda and Pietro Maximoff meet with Ultron, they join his quest to destroy the Avengers. Holding a grudge against Tony Stark, the twins aid the AI in manipulating the team, hitting them where it hurts most. The Maximoffs believe that Ultron simply wants to eliminate the Avengers but the truth is much darker.
In reality, the robot wants to eliminate the entire world, justifying his actions by relying on that old trope about having to destroy first and create second. Ultron exploits the twins' loss and pain to use their powers against the Avengers, and once they realize it, they join the battle against him.
Obadiah Wants To Kill Tony
At the beginning of his MCU journey, Tony sees Obadiah Stane as a friend and colleague, but mostly a mentor and substitute father figure. Stane, Stark Industries' second in command, wants to take over the company and plots Tony's kidnapping and eventual assassination. His plan backfires when Tony builds the Iron Man suit and escapes mortal peril.
Obadiah's role as the villain isn't surprising to the audience. However, it is to Tony, and seeing one of the most important people in his life turning against him is certainly a blow for the genius, billionaire, playboy, philanthropist.
The Ancient One Uses Power From The Dark Dimension
Mystical, domineering, and almost ethereal, the Ancient One is a mentor to every and any student at Kamar-Taj. She is wise yet mysterious, approachable yet distant. Because of her vast knowledge, she is an enigma to nearly everyone around her.
The Ancient One is one of the most complex characters in the MCU. She knows what she has to do and understands that sometimes rules need to be broken or bent to win the war. Still, her use of the Dark Dimension power to sustain her long life is seen as a great betrayal, and Mordo becomes disillusioned by her and sorcery as a whole.
S.H.I.E.L.D. Uses The Tesseract To Build Weapons
One of the major plot points of the first Avengers movie is S.H.I.E.L.D.'s duplicitous nature. After Thor's visit to Earth, the powers that be decide that Earth needs a higher defense system to fight the Gods and monsters that are rapidly spawning.
S.H.I.E.L.D.'s use of the Tesseract to create weapons of mass destruction is an astoundingly misguided plan. As Thor says, it's just a sign that Earth is ready for a higher form of war. The fact that S.H.I.E.L.D. seems to see everything in war terms is troubling at best and a clear sign that not everything is as it seems with the organization.
Hail Hydra!
And speaking of S.H.I.E.L.D., Captain America: The Winter Soldier reveals just how corrupted the organization truly is. Alexander Pierce, Secretary of the World Security Council, is truly an agent of Hydra responsible for sowing chaos around the world to have people willingly surrender their freedom in exchange for security.
Pierce comes dangerously close to fulfilling Hydra's goal. He succeeds in fooling the entire world, living a long and full life of crime and chaos. Pierce and Hydra prove to be incredibly cunning and ruthless, making everyone around them, including Nick Fury, look like amateurs.
N'Jobu Sides With Klaue
The younger brother of King T'Chaka, N'Jobu is a Wakandan spy in Oakland, California. Because of his exposure to the outside world, N'Jobu becomes radicalized. He comes to see Wakanda's isolation as a mistake and wants to use vibranium to initiate a global revolution for people of African descent.
N'Jobu's extremist views lead him to side with Ulysses Klaue, revealing Wakanda's existence to him and aiding him in stealing a cache of vibranium. The attack results in the death of several Wakandan citizens, which in turn leads to N'Jobu's fall from grace and eventual death.
Nearly Everything Loki Does
If there's one character in the MCU that's a synonym with treason, that's Loki. He is the God of Mischief, after all, and he more than lives up to his title. Time and again, Loki betrays his older brother, succeeding in fooling the God of Thunder nine out of ten times.
Loki isn't necessarily evil, he's just a narcissist misanthrope who wants to be King at any cost. Loki does have a soft side that comes to light now and then. However, and considering he's literally a mass murderer, redemption is probably something that he couldn't achieve in one lifetime.
Nebula Betrays The Avengers
It's not exactly fair to say that Nebula betrays the Avengers, because it's not actually Nebula who does it. Instead, it's her past self, the one still blindly loyal to Thanos, who turns her back on Earth's mightiest heroes and brings the Mad Titan and his army into the future.
Present Nebula can do nothing but watch as her past self ruins the time heist with some time shenanigans of her own. The betrayal complicates things for the Avengers and nearly provokes a second, more lethal Snap. Alas, things work out in the end when the Avengers finally assemble.
Steve Lies To Protect Bucky
Steve's relationship with Bucky Barnes is a complicated one. More than a friendship, Steve and Bucky share a bond that no one else, not even the audience, can fully comprehend. In a way, they're the love of each other's lives. Whether it's romantic or not is a different issue, but the point is, they're both willing to die for the other.
Once he discovers the truth about Bucky's involvement in Tony's parents' deaths, Steve keeps it a secret, condemning himself in the process. His mistake provokes a giant rift in the Avengers that can only be solved once the Mad Titan's threat is imminent, and is not only a giant betrayal of Tony's trust, it's also the most cowardly thing he ever did.