During the Titan Wars, MacAllan served as XO on the Andromeda-Class Carrier IMS Odyssey, becoming good friends with his commanding officer Marcus Graves and engaging in multiple war games exercises during this time. However, a rift would soon develop between the two due to MacAllan's grievances with the IMC's treatment of Frontier citizens, and the brutality enacted upon those who attempted to resist. This split would eventually result in a mutiny, with a large portion of the Odyssey's crew. Due to their friendship, Graves would allow MacAllan to commandeer the ship, though later claiming he was forced out when questioned by the IMC. MacAllan would crash the Odyssey on the thus-unexplored planet Troy, and building a small town in the wreckage.
During Titanfall, MacAllan is found in the second mission, The Colony, when the distress signal of the colony created by the crew of the IMS Odyssey is picked up by Militia forces following the events of The Refueling Raid. Angered by the IMC's attack on the colony and the needless massacre of the civilians there, MacAllan agreed to the request of Sarah and Bish that MacAllan lead the Militia due to his experience with one stipulation: that the Militia save the civilians there. Upon completion of this goal, MacAllan told them that he can help them beat the IMC in the Frontier, but that he needed the information stored on the Odyssey. In the mission Odyssey, the Militia distract the IMC forces long enough for MacAllan to retrieve the information on the IMC's facility at Demeter. MacAllan slowly reveals his plan to destroy Demeter which begins with retrieving his old comrade, Robert "Barker" Taube from Angel City. In the mission Get Barker, MacAllan sneaks Barker out of the city through the sewers while the Militia forces combat the IMC soldiers on the surface. This culminates with the arrival of the IMS Sentinel, which MacAllan orders to be attacked by the Militia's Hornet fighters, albeit under protest by Bish and Sarah. The attack damages the IMC Carrier, thus requiring it to be sent to dry dock for repairs. This is part of MacAllan's plan, using the defense guns of Outpost 207 to destroy the Sentinel in Assault on the Sentinel.
The second step in MacAllan's endgame is to find a weakness in the Repulser towers which protect Airbase Sierra in the Demeter system. To do this, MacAllan has Barker navigate the Militia forces to Boneyard where the former IMC facility, Base Golden is located, with one of the towers. During Here Be Dragons, the Militia ground forces gain the information needed to disrupt the operations of the towers before the IMC forces scuttle the facility. With the information in hand, MacAllan orders the all out assault on the Demeter system, beginning with the attack on Airbase Sierra. In The Three Towers, MacAllan orders the Militia soldiers to create a diversion so Sarah and her covert assault team can take down the Repulser towers and let the wildlife devastate the facility. This clears the path to the facility on Demeter itself.
In the second-to-last mission, The Battle of Demeter, MacAllan leads the pilots into battle and infiltrates the inner reactor. Sergeant Blisk pursues him, under orders from Graves, and due to the fragile nature of the reactor, is forced to engage MacAllen in hand-to-hand combat only. MacAllan locks himself in the reactor, and begins to overload it, causing the destruction of Demeter. Blisk retreats on Graves' orders while the Vice Admiral pleads with MacAllan to stop. As his final request, MacAllan requests Graves join the Militia and lead them because MacAllan would not be able to. MacAllan's final words are addressed to the Militia pilots, telling them that it had been an honor serving with them. With that sentiment uttered, Demeter explodes, killing MacAllan and all Militia and IMC forces there.
Due to MacAllan's status as a war hero and in honour of his sacrifice, MacAllan's name was given to the Militia's new line of MacAllan-Class Carrier and its flagship vessel the MCS James MacAllan. In addition, at least two Militia Pilot groups; MacAllan's Marauders and the Glory Blazers, bear MacAllan's name in their emblem or name.
- MacAllan appears on wanted signs in Angel City in both Titanfall and Titanfall 2, with a bounty of 100,000 credits. As of Titanfall 2, the sign has been updated to reflect MacAllan's status - with the word DECEASED replacing the bounty, perhaps as an example to intimidate Militia sympathizers.