Assassin's Creed traditionally attempted to make the players question their own actions throughout a game. The first title, released in 2007, presented lots of philosophy and challenged the player to question who the bad guy really was in certain scenarios. Though the series has always had completely evil villains, it's also known for gray characters as well. Even the mysterious "First Civilization" is neither truly good nor evil, although there are exceptions to each.
Even the titular assassins of Assassin's Creed aren't always the good guys, although they are nearly always the protagonists. When crafting the historic epics, the teams at Ubisoft are careful to write plenty of characters that really make the players think about their positions in the game world. Some villains were bad to the core, while others weren't always the villains they became, and many were simply in a gray area.
Spoilers for the Assassin's Creed franchise ahead!
8 Alfred The Great
Alfred the Great actually helps Eivor throughout the campaign of Assassin's Creed: Valhalla. Alfred was the leader of Wessex and eventually the leader of all of England and helped repel multiple Viking incursions. He was also the leader of the cult known as the Order of Ancients, an evil group of cultists established during the events of Assassin's Creed: Odyssey. Though this group has already been set to be quite evil, Alfred himself is unhappy with it.
Alfred wants to disband the Order of Ancients and replace it with something better. As Alfred puts it, "more in line with the ebb and flow of nature." Though Alfred sought the destruction of the Order, he still revered the Father of Understanding, a key figure in the Order's mythos. This same Father of Understanding is the key figure behind the main foes of the Assassin's Creed franchise: the Templar Order. That's right, Alfred the Great helped rid the world of the evil Order of Ancients, but his replacement would eventually become the infamous Templar Order.
7 Elise de la Serre
Elise de la Serre is the forlorn Templar love of Arno Dorian, and she is another example of a strong female character in the franchise. Though not inherently evil, Elise was often at odds with Arno thanks to the two falling on opposing sides of the secret war between Assassins and Templars. Elsie blamed Arno for the death of her father and hated him for it. Though Arno wanted nothing more than to prove the truth, Elise was distant in part thanks to their allegiances.
Elise's views were heavily based upon knowledge she gained from the former Templar leader, Haytham Kenway. Eventually, she sought to bring the warring factions together, and with the help of Arno, the two were able to right at least some of the wrongs by both the Assassins and Templars of France. Ultimately, Elise and Arno were able to work together, making her less of a villain to Arno and more of a chaotic force in his life.
6 Benjamin Church
Benjamin Church was a high-ranking Templar during the American Revolutionary War. He was a self-serving surgeon with quite an ego. While he was a rather despicable person, his actions and reasons for eventually becoming a traitor to the Templars leave Church in a gray area. Church was responsible for rooting out corruption within the Templar order and even assassinated a prolific slave trader within the Order.
As he fought for both the Templars and the Continental Army, Church eventually became angered by both. He saw no just path in what either side was doing, and betrayed both, causing the leader of the Templars Haytham Kenway to employ his Assassin son Connor in capturing Church. Once captured, Kenway tortured Church before Connor stepped in and swiftly assassinated him. Church warned Connor that no path was absolutely just or fair, and that life was much more complicated than that.
5 Achilles Davenport
It's hard to imagine the wise former Assassin master Achilles as a villain after players saw him train Connor like his own son in the events of Assassin's Creed 3, but Achilles was once a greedier man. Before Assassin's Creed 3, Achilles was a high-ranking Assassin mentor in Assassin's Creed: Rogue. He trained a man named Shay Cormac, the protagonist of Rouge, and entrusted Shay with his most important mission: discovering Isu Temples.
In a sort of 1700s Cold War, the Assassins and Templars were racing to discover temples left behind by the First Civilization, the Isu. Shay found one of the temples for Achilles but disturbing it caused an earthquake that killed thousands. Shay returned home and confronted his mentor, but Achilles wouldn't hear anything from Shay. These actions led Achilles into becoming Shay's enemy, and after the Assassins attempted to kill Shay, he went rogue and joined the Templars. Shay would go on to destroy the entire Colonial Branch of Assassins, and it was all thanks to Achilles' mistakes and greed.
4 Shay Cormac
Once a promising recruit of the Colonial Assassins, Shay Cormac would eventually spiral into a Templar ally known as the "Assassin Hunter." Shay felt like he had been lied to by Achilles, the assassin that had trained him. After being shot and falling into the ocean, Shay was strong enough to survive and was rescued by Templar forces.
It's hard to call Shay a villain after how he was treated by the Assassins, but his later actions in France led to the beginning of the French Revolution. Shay was responsible for killing Arno Dorian's father, orphaning the child, and causing an all-out civil war in France. Shay was following his heart in joining the Templars because he didn't want to find any more Temples and cause any more innocent deaths, yet his final act in the series of killing Arno's father ultimately led to countless innocent deaths.
3 Haytham Kenway
Arguably the most important character of the American Revolution arc in the Assassin's Creed timeline, Haytham Kenway stood as one of the most influential and powerful Templars in the series. He was originally trained as an Assassin, but many events led to his recruitment into the Templar order at a young age. Haytham strived for peace--albeit peace through control. He believed that people yearned to be led, and that strong leaders were necessary to keep the peace. And what stronger leader than the Templar Order?
Haytham was ruthless in his work, and his enemies were often felled beneath his blade. He assisted the natives on the American Frontier, even killing fellow Templars he believed were out of line. He even worked with his son Connor, an Assassin, when he felt it benefited him and his goal of ultimate peace. Yet, his vision of peace was twisted, and he eventually fell to his own son, Connor. Dying in Connor's arms, Haytham admitted that he was proud of his son, but still maintained that Connor was disillusioned with how to achieve peace.
2 Deimos
Called a demi-god by the Order of Ancients, Deimos is the sibling of either Kassandra or Alexios (depending on whom the player chooses to play as) in the story of Assassin's Creed: Odyssey. The great Spartan soldier Nikolaos was going to sacrifice Alexios because he was prophesied to bring about the fall of Sparta. In an attempt to stop her father, Kassandra tackled him. She was deemed a traitor to Sparta, and she was thrown from the cliff alongside her brother.
One of the children (again, depending on who the player chose to play as) was taken in by the Cult of Kosmos, the precursors to the Order of Ancients. They were trained and told they were a demi-god by the name of Deimos. Deimos endured a horrible childhood of abuse that brainwashed them into a weapon of the Cult. Though they become the main villain of the game, it can easily be said that they weren't always evil and were instead twisted by the true villains: The Cult of Kosmos.
1 Al Mualim
The mentor of the original protagonist, Altair, Al Mualim is a truly gray character. He secretly worked with the Templar Order to obtain a Piece of Eden, betraying his entire order of Assassins to do so. Yet, Al Mualim's teachings were particularly impactful on Altair and the entire Brotherhood. His philosophies and teachings laid the groundwork for all of the Assassins that would follow the Creed in the future.
Al Mualim acts as both the mentor and the final boss of the original Assassin's Creed and this places him as one of the definitive examples of a villain that wasn't always evil. His actions were deplorable, but without him, Altair never would've reached his own true potential.