Harlan Cunningham proves to be an extremely skilled Assassin, not only managing to ambush and almost completely route several teams of Templar agents to allow William's cell to escape, but he also leads a team in infiltrating and escaping Abstergo Industries Rome headquarters to kill a team of hackers and destroy their servers. This is the same building that a previous team of Assassins were slaughtered attempting to enter in Assassin's Creed I.
Emmanuel Barraza figures out via a few minor clues and a few overheard comments in Japanese (a language he barely speaks) that the Onmoraki-Gumi are actually Assassins, and sticks his hand in front of a hidden blade strike meant for Gavin before calmly defusing and explaining the misunderstanding to all involved.
During the Altair II crew's trip to Russia, they meet the only Assassin left in Russia, Galina Voronina, who takes them to the last Assassin base in the country. Everyone there has been driven insane by the Animus and it's up to Galina to kill her way left and right through her former comrades, one of them being her twin sister, all of which plays like a PC slicing through mooks.