Both Gavin and Susan Drayton, the ship's captain, had worked together to steal the Altaïr II, though they possessed different intentions at first - Susan's motivation was to combat Japanese whalers, while Gavin aimed to turn it into the mobile Assassin headquarters it now serves as. However, due to Gavin not having the necessary skills to properly captain the ship, Susan was given the position instead.
From 14 to 19 May 2013, the Altaïr II traveled through the Pacific ocean, before dropping off Shaun Hastings and Rebecca Crane in California. During a transfer of power from William Miles to Gavin as Assassin leader, Gavin used a book given to him by William in order to discover the Assassin locations around the world.
After the Altaïr II stopped at Honolulu Harbor on 11 September 2013, Gavin failed to contact the Osaka Assassins. The ship traveled to the Philippines on 1 October 2013, where Emmanuel Barraza, the weapons instructor, re-armed the Altaïr II crew to prepare for a potential fight in Osaka.
By 1 December 2013, the ship had docked in Osaka, Japan, where it stayed until 1 January 2014, when the Altaïr II was taken to Tokyo for New Years. During the ship's stay in Japan, its crew were busy discovering and rebuilding the Osaka brotherhood, after which they celebrated the holidays.
By 19 February 2014, the Altaïr II had docked in Vladivostok, Russia. After a clue in the book leading to the ship's crew discovering the location of the Russian Assassins, the Altaïr II sailed around Russia in order to dock in St Petersburg. During this time, Gavin, Emmanuel, and Emmett left the ship, and went into mainland Russia in order to find the Russian Brotherhood's location.
Finland and Norway
By 10 May 2014, the Altaïr II had docked in Helsinki, Finland, where Gavin gave the crew members the order to find William Miles, using clues from the latter's book. Having uncovered the location, the ship then left and by 1 May 2014, the Altaïr II had arrived at William Miles' bunker in Norway.
Discovering bugs reporting the Assassins' activities to a group called the Initiates, William interrogated each member of Gavin's crew on a daily basis, until all suspects were seen to. Upon gathering their testimonies and reviewing the information over the course of several days, William gathered the crew and subsequently ordered Galina to kill Dr. Stephanie Chiu. Suddenly, Eric Cooper leapt to her defense, explaining he was the spy – however, Stephanie countered this claim by admitting her involvement through uploading his reports. Despite their intervention, William explained the order to simply be a ruse, deciding that the two Initiates were reasonable people and did not deserve execution.
In late 2018, the Altaïr II was lended to an Assassin cell comprising Layla Hassan, Victoria Bibeau, Kiyoshi Takakura, and Alannah Ryan, who used it to travel to the Greek island of Santorini in their search for Atlantis. Later on, they travelled to mainland Greece in order for Layla to locate symbols needed to unlock the seal on Atlantis' gate. After returning to the Santorini with Layla in the vault to Atlantis, the Altaïr II was boarded and attacked by the Sigma Team. Despite being wounded, Kiyoshi was able to fend off the attackers. Fearing for Layla's safety, they made the decision to go off the radar, leaving Layla alone.
- Gavin Banks - Assassin leader
- Susan Drayton - Captain
- Alannah Ryan - Historian
- Eric Cooper - Navigator, supervisor
- Layla Hassan - Archaeologist
- Emmanuel Barraza - Armorer, weapons instructor
- Victoria Bibeau - Psychiatrist
- Emmett Leary - Computer expert
- Dr. Stephanie Chiu - Medic
- Nodar Ninidze - Chief steward
- Kiyoshi Takakura - Guardian
- Akaki Ninidze - Chief engineer
- Galina Voronina - Enforcer
- The registry number of the Altaïr II is NCC-1701-D. This is a nod to the Star Trek: The Next Generation series, as it is the registry number of the USS Enterprise-D.
- The name Altaïr II is a reference to both the brightest star in the constellation Aquila, and the Assassin Altaïr Ibn-La'Ahad.