- Charles Lee: "Why do you persist...? You put us down. We rise again. You end one plot – we forge another. You try so hard... But it always ends the same. Those who know you think you mad and this is why... Even those men you sought to save have turned their backs on you. Yet you fight. You resist. Why?"
- Ratonhnhaké:ton: "Because no-one else will!"
- ―Charles Lee and Ratonhnhaké:ton discussing the conflict between their factions, 1782.[src]
The Assassin–Templar War is an ideological, sometime military, conflict between the Assassin Brotherhood and the Templar Order, that has spanned across the entirety of known human history. The two factions often took part in, or even precipitated, military conflict between nations to further their own agendas within their war, largely in the shadows of conventional politics.
The origin of the conflict is believed to stem from the killing of Abel by his brother Cain, to obtain his brother's Apple of Eden. However, more plausible explanations for the start of the war can be found in the aftermath of the Human-Isu War. The Assassin-Templar War was largely fought by proxy, with each side manipulating national governments and powerful organisations in order to achieve each own aims.
After the Toba catastrophe, the surviving human leaders came into possession of several Pieces of Eden, and debated on how to best use them for humanity's benefit. They were aware of their former slavers interfering with their evolution, and sought to lead humanity on their destined path by any means necessary. In order to achieve this, they utilized the Pieces of Eden as tools, but were distrustful of any who attempted to make peace with the First Civilization. 
However, others wanted to give humanity complete freedom, and envisioned a world where all beings could live according to their own will. As such, the maxim "Nothing is true, everything is permitted" became their philosophy, exemplifying the belief that all were free to determine their own path. They also believed that the misuse of the Pieces of Eden to control others was against all they had worked and suffered for, as it would enslave humanity once more. 
It was rare for the conflict to ever become particularly conspicuous, although there were occasions, such as the Third Crusade, where the Assassins and Templars openly fought alongside those they were manipulating. Another example was during the Golden Age of Piracy, where many Assassins attempted to apprehend the Sage Bartholomew Roberts from a Templar convoy, ending in a giant battle in the streets of Havana.
Throughout the conflict's long history, a number of different powers became involved, such as the fledgling United States, the early Soviet Union, the Aztec, Inca, Sikh, Ottoman, French, and Holy Roman Empires, aligning themselves with the Assassins, while the Papacy controlled by the House of Borgia, the Byzantine, Russian, Portuguese, Spanish, and British Empires, the Confederate States, modern United States, and Nazi Germany, supported the Templars. These alliances were rarely permanent, however, and often changed along with the leadership of a particular group.
By the 20th century, the conflict had largely removed itself from the public view, with the Templars operating principally through their front companies, like Abstergo Industries and the Abstergo Foundation Rehabilitation Center, while the Assassins struggled to survive on the fringes of society, living in secluded communes.
The length and devastation of the war had a significant effect on the plans of the Capitoline Triad to avert the Second Disaster. In the Grand Temple in 2012, Juno commented to Desmond Miles that the two factions had wasted centuries by squabbling over Isu artifacts; time which could have been spent on locating the Temple and continuing the work meant to save the world from the solar flare.
Assassins and Templars
Historically, the Assassins and Templars were not above working when confronted with a common obstacle or purpose. An early example of such an alliance involved the Levantine Assassin Altaïr Ibn-La'Ahad and the English Templar Maria Thorpe, who worked together to bring down Armand Bouchart, although their motives were initially vastly different.
During a Maroon rebellion in Port-au-Prince, the Assassin Adéwalé was led to helping brothel owner, and Templar ally, Bastienne Josèphe defeat the murderous and merciless Marquis de Fayet, an infamous slave trader that had ordered a French ship to destroy an approaching slave ship during the rebellion. Following de Fayet's death, Adéwalé left Port-au-Prince, but relinquised Precursor box that Bastienne sought into her care. Sometime later the two met once more and had a son. Their grandson, Eseosa, became an influential part of the final Maroon rebellion, the Haitian Revolution and later joined forces with the Colonial Assassin, Connor.
Another notable alliance occurred during the American Revolutionary War. When Benjamin Church turned on the Colonial Rite of the Templar Order, the Grand Master of the Rite, Haytham Kenway, pursued him with the help of his son, the Assassin Connor, whose aim was to recover the supplies stolen by Church, meant for George Washington's forces stationed at Valley Forge. After Church's death, the pair continued to work together, in order to allow the colonies to gain independence from the British Empire. However, when Haytham revealed Washington's intent to attack Connor's village of Kanatahséton for a second time, the Assassin severed ties with both of them.
During the French Revolution, the Assassin Arno Dorian and his adoptive Templar sister Élise de la Serre hunted the Templar Grand Master François-Thomas Germain, heir to François de la Serre, who he replaced after a his predecessors assassination during the former's coup d'etat. François de la Serre had sought to maintain a truce between the Templars and Assassins, which was one of the reasons for his death. Such truces, however, were short-lived, since the leaders that succeeded those who brokered them, rarely honored the truce. Mirabeau, the Mentor of the French branch of the Assassin Order, was poisoned by Pierre Bellec, who held a fanatical belief that peace between the two factions was impossible.
In 1868, the Assassin Jacob Frye temporarily aligned himself with the Templar Pearl Attaway, against Malcolm Millner and her cousin, the Grand Master of British Rite of the Templar Order, Crawford Starrick. Jacob was unaware of Pearl's true allegiance however, and immediately resolved to assassinate her upon his discovery.
In 2016, Templar Victoria Bibeau and Assassin Griffin agreed to a ceasefire so they can stop Templar turncoat Isiah from acquiring the third prong. 
Besides working with Templar defectors, the Assassins also caught the attention of other organizations. During the Renaissance period, Mario Auditore led a band of mercenaries during various assignments for the benefit of the Brotherhood, such as the attack on Vieri de' Pazzi in San Gimignano.
In Venice, and later Rome, Bartolomeo d'Alviano led a company of mercenaries allied with the Assassins. Several brothels in Italy were led by Assassins, including Paola, Teodora Contanto and Claudia Auditore da Firenze, operating in Florence, Venice and Rome, respectively. Some of the thieves groups were led by Assassins, such as La Volpe and Antonio de Magianis. However others, such as the Cento Occhi in Rome, opted to stand with the Templars. Centuries later, some of the pirates of Nassau, such as Benjamin Hornigold, Josiah Burgess, and John Cockram also sided with the Templars. Another pirate, known as Le Chasseur, helped the Colonial Brotherhood during the Seven Years' War, but was killed by the Assassin-turned-Templar Shay Cormac before he could be inducted into the Assassin Order as a member.
In modern times, other organizations have taken notice of the conflict between the Assassins and Templars, such as the Initiates, a group of unidentified individuals with vast resources and connections, who eventually allied themselves with the Brotherhood. The hacker collective, Erudito, worked to uncover Abstergo Industries' plots to control humanity; one of their notable activities was hacking the Liberation video game developed by Abstergo Entertainment using edited versions of Aveline de Grandpré's genetic memories. While Abstergo planned to omit all references to the Templars and discredit the Assassins, the Erudito hacks allowed the user to see the original footage and learn the truth.
The Templars also came into contact with the Instruments of the First Will, a group who wish to grant control over humanity to Juno, who was now freed from her imprisonment in the Grand Temple following Desmond Miles' sacrifice in 2012. The Master Templar Juhani Otso Berg suggested using the Instruments to acquire Pieces of Eden, while the other group siphons Templar resources to achieve their own plan. However, the Templars do not consider the Instruments of the First Will to be a threat, and do not prioritize eliminating Juno, either.
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5 Assassin's Creed II
- ↑ 2.0 2.1 2.2 2.3 2.4 2.5 Assassin's Creed
- ↑ 3.0 3.1 3.2 Assassin's Creed: Revelations
- ↑ 4.0 4.1 Assassin's Creed IV: Black Flag
- ↑ 5.0 5.1 5.2 Assassin's Creed III
- ↑ Assassin's Creed: The Fall
- ↑ Assassin's Creed (Titan Comics)
- ↑ Assassin's Creed: Brahman
- ↑ 9.0 9.1 9.2 9.3 Assassin's Creed: Rogue
- ↑ Assassin's Creed: Project Legacy
- ↑ 11.0 11.1 11.2 11.3 11.4 Assassin's Creed: Brotherhood
- ↑ Assassin's Creed: The Fall
- ↑ Assassin's Creed: Last Descendants
- ↑ Assassin's Creed: Bloodlines
- ↑ Assassin's Creed IV: Black Flag - Freedom Cry
- ↑ Assassin's Creed: Initiates - Eseosa's Codex
- ↑ 17.0 17.1 Assassin's Creed: Unity
- ↑ Assassin's Creed: Syndicate
- ↑ Assassin's Creed III: Liberation