As Abstergo Industries' Animus recruits progressed through the Animi Training Program, select individuals were chosen to progress to the second stage, as they had an increased adoption rate for the skills which the scheme aimed to instill into their subjects via the Bleeding effect. Following this, they would be supported into becoming Master Templars by Abstergo, via documents and videos provided for them.
Like the first stage operated, influential Templars from the Ottoman Renaissance were selected for use as Animi Avatars. For some Avatars, their historical counterparts were found and assassinated by the Assassin Ezio Auditore, as he trained his apprentices in Constantinople into becoming Master Assassins, along with those he had killed following his journey to discover about Altaïr Ibn-La'Ahad's hidden library.
- Bombardier - Secretly a member of the Qizilbash, an anti-Ottoman rebel group that had close ties to the Templars, the Bombardier portrayed himself as a member of the Ottoman artillery corps in order to sabotage them from within. He carried a mace as his specialty weapon.
- Brigand (DLC exclusive) - A daughter of a rich noble, the Brigand stole relics and traded secrets from her targets, as well as ruthlessly pursuing those who dared to betray her, in order to earn wealth by serving the Templar cause. Her specialty weapon was a spear.
- Champion - A renowned professional fighter after years of brawling in tournaments throughout the mountainous region of Thrace, the Champion earned the Templars' esteem and the right to fight for the red cross. He wielded a small axe as his specialty weapon.
- Corsair (DLC exclusive) - A ruthless pirate who sailed the seas, the Corsair would wait for her victims to emerge from their travels, before she and her loyal crew confronted them and stole their valuables, much to the Templars' profit. She carried a thin cutlass as her specialty weapon.
- Courtesan (Loyalty exclusive) - A courtesan born into the intrigues of the Templars, she moved around Constantinople like a sultry shadow. Her weapon of choice was a bladed fan, wielded like a dagger.
- Count - An infamous Wallachian ruler feared for being brutal in torture, he was given the nickname "the Impaler." There were also many rumors of him being a vampire, due to his pale skin and bloodthirsty personality, contributing to his infamy. His specialty weapon was a bladed mace.
- Crusader (Pre-order and DLC exclusive) - A traitor of the Assassin Order and a secret Templar agent, the Crusader held Al Mualim and other Assassins hostage after a siege of Masyaf's fortress, though he failed, as he was assassinated by Altaïr Ibn-La'Ahad. He carried a claymore as his specialty weapon.
- Deacon - Previously a member of the Eastern Orthodox faith, the Deacon renounced his beliefs after being publicly embarrassed and humiliated by the Patriarch of Constantinople. Managing to retain a nominal position for himself, he used his standing to erode the church from within for his own personal vengeance, as well as the Templars' benefit. His specialty weapon was a kilij, a Turkish long sword.
- Gladiator (DLC exclusive) - A bloodthirsty warrior who was orphaned and sold into slavery at a young age, the Gladiator was forced to compete for his life to entertain crowds. His soon famous position gave him a spot in the Templars to shed blood on their behalf. His specialty weapon was a spatha, a Roman long sword.
- Guardian - An estranged cousin of a distant Sultan of the Sennar Sultanate, the Guardian assigned himself the role of watching over the Templars' secrets, in order to protect their ideology that he believed so fervently in. He remained devoted to their cause having discovered their principles in Alexandria, once his family had disowned him. He wielded a lance-like spear as his specialty weapon.
- Knight (Uplay exclusive) - A knight who, inspired by his hero, blindly joined the Templars under their cause. Determined to re-image himself and the world in his patron's design, he eliminated anyone who oppressed their ideology. His weapon was a titanic greatsword.
- Ottoman Doctor (Pre-order and DLC exclusive) - A Venetian expatriate who had hopes of becoming a successful doctor, he unfortunately developed a bad habit of killing his patients. He wielded a bladed syringe, filled with his own mercury solution, which he used as a dagger.
- Ottoman Jester (Pre-order and DLC exclusive) - A Venetian expatriate who had a taste for bold adventure, the Ottoman Jester joined the Borgia after his antics caused the ruin of a Sultan's beloved vizier. He was tasked to perform as an entertainer at the Topkapı Palace, in order to destabilize the Ottoman dynasty from within, and acted as a free agent for the Templars after the Borgia's downfall. He used a khanjar dagger as his specialty weapon.
- Privateer (DLC exclusive) - A pirate of the seas who knew no master nor morals, the Privateer helped both Templars and Assassins alike charter his ship, for money was his true motive. He carried a basket-hilted cutlass as his specialty weapon.
- Renegade (Singleplayer unlock) - Born into an oppressed tribe in Eastern Anatolia, the Renegade became familiar with the Templars at an early age, after the results of an ambush had left him as an orphan. Instilled with a strong hatred for the Ottoman Turks, it was only his fierce determination and loyalty to the Templars that allowed him to take out their opposition and eliminate all who went against their ideology. He wielded a soliferrum-like spear as his specialty weapon.
- Sentinel - A Wallachian noble recruited into the Assassin Order, the Sentinel joined the Templars after his Order made peace with the Ottomans, resulting in him feeling betrayed. With his separation from the Assassins, he used it as a chance to strike back against them, much to the Templars' benefit. He wielded a long katar as his specialty weapon.
- Thespian - As a wealthy Byzantine woman, the Thespian lived a life of luxury and nonchalance in the high society of Constantinople. She was often delivered in the arts and other delights at the request of the Templars, using her seductive charisma to influence the Ottoman officials and visiting royalty in return. She used a dagger as her specialty weapon.
- Trickster - After many years of abuse and ridicule, the Trickster became a con artist, using her guise as a Romani fortune-teller to trick citizens out of their money. She also proved to be the Templars' link to a vast underworld of criminal activity. Her specialty weapon was a dagger.
- Vanguard - A Cossack from Odessa, the Vanguard joined the Templars after her military service of protecting her homeland from the Ottomans ended. Accepting promises of wealth and power, she used her skills as a scout and a spy towards the Templars' cause. She possessed a small hatchet as her specialty weapon.
- Vizier - Once a famous and respected officer from Eastern Anatolia, along with previously being a loyal servant of Sultan Bayezid II, the Vizier embraced the Templars' philosophy as being the only way of bringing order and international glory to a world where chaos and mediocrity were the norm, once the Sultan's ambitions to conquer the world subsided. He carried a sheathed sword as his specialty weapon.