- "You're one of a kind. Benevolent, they say. All castes and creeds under one roof. You haven't even the temper to order the death of one lowly thief. It takes more nerve than that to bring the world to order."
- ―Francis Cotton to Maharaja Ranjit Singh, 1839.[src]
During the 1830s, Cotton was assigned to accompany William Hay Macnaghten, the aide to the British Governor-General to India, Lord Auckland. It was through this position that in 1839, Cotton visited the Summer Palace in Amritsar, India, to attend the royal court of the Maharajah Ranjit Singh, ruler of the Sikh Empire. Cotton plotted to poison the Maharajah so the British, and by extension the Templar Order, could take control of India.
Upon arriving, he spotted the Assassin Arbaaz Mir posing as a Kashmiri emissary, Cotton became aware of Mir's that it was an Assassin through his movements, but he did not know that he was posing as an emissary nor that he intended to steal the Koh-i-Noor to prevent it from sailing to Britain. Confronting the Assassin, he was told the two had no need to fight at that event, as Arbaaz had his own reasons for wanting the Maharajah dead. Cotton was skeptical of the Assassin's claim, and suspected that he had another agenda, although he shared with his enemy his personal disgust of the ailing Singh. Sometime later during the function, Cotton spied on Arbaaz's attempts to locate the Koh-i-Noor diamond in the vaults beneath the palace.
Alerting the palace authorities to the theft, Cotton had Mir imprisoned, and used the good will generated by this act to gain a private audience with Singh alongside Macnaghten. Cotton poisoned the Maharajah's drink, but the meeting was interrupted by Arbaaz, who had been freed from the dungeon by Pyara Kaur. Cotton fought off the Assassin, who attempted to warn Singh of the poison, but Cotton gloated that he was too late and that Singh already drank from the cup.
The Maharajah managed to rise and declare that India would never fall to the Templars. Cotton held his sword up to Singh and warned him to stay back, noting it was a shame to kill him since he was supposedly a wise and benevolent ruler. He derided him as too weak to bring order to the world, and then preceded to again set the guards on the Assassin, claiming he was trying to take the Maharajah's life.
Cotton fled the throne room as Arbaaz fought against the guards, encountering Pyara Kaur attempting to escape the palace with the Koh-i-Noor. Mistaking her for an Assassin due to her hood, Cotton raised his knife to stab her, but was leapt upon by Raza Soora, who wounded Cotton by scratching his face with his fingernails. Cotton threw Raza off of him and angrily declared the Assassins to be vermin who needed to die.
Before he could stab Raza, Pyara activated the Koh-i-Noor, causing her to become possessed by a member of the First Civilization, who began speaking a cryptic message about humanity being fragmented and to hide the Koh-i-Noor until they were united. Cotton drew his gun and fired upon the being, hitting the Koh-i-Noor in the process, creating an energy blast that killed him.
- It was inferred by Cotton that, similar to Templars such as Haytham Kenway and Julien du Casse, he was one of the few in the Order to possess at least one Hidden Blade, obtained as trophies of the Assassins he had killed.
- In 2015, his name was on a list of known British Templars used by the Templar Isabelle Ardant.