When Harlan was in high school in Texas, he was a promising wrestler, but his career was put to an end when he was outed as a homosexual. He then fled to Europe and looked for solace in the Assassin Brotherhood, where he was assigned to Adriano Maestranzi's Florentine brotherhood. Gavin Banks altered official records to hide most details of his life before joining the Assassins.
Assisting William Miles
In late September and early October 2012, Harlan exchanged text messages with William Miles to be updated on his journey to Switzerland, to which he informed Adriano Maestranzi on William's progress. He later secured Desmond Miles, Shaun Hastings and Rebecca Crane from the Colosseum Vault with William's help, and reluctantly returned Desmond to the Animus after Juno's possession of him caused him to go into shock.
As William's team attempted to flee Italy, Harlan received a text from William on 16 October, telling him that the Templars were onto them and that they were going into hiding. On 25 October, Harlan was again contacted by William, who asked for his assistance in escaping Italy. At 9:51am on 27 October, Harlan led an ambush on Abstergo's tactical Delta Team, killing several of the Templar agents and allowing William's team to escape from the Templars' tail. Harlan sent William a text at 10:38am, informing him that they only lost one Assassin in the skirmish, and that one of the Templars had "lost it" during the battle.
A few weeks later, Harlan texted William on November 9, telling him that everything was going according to plan and that the Templars did not known where William's team was. He then passed on a message from Adriano, who wanted to know if William's team had made any progress.
Striking at the Templars
On 28 November 2012, at 5:08pm, Harlan sent a message to William from the Provincial road SP11 in Italy, informing him that they had infiltrated the Abstergo campus and killed four hackers along with some guards, and destroyed their servers, which meant Abstergo could not track William. After returning to the safe house in Florence on 29 November, Harlan discovered that he or another member of the cell had been tracked back to the base. He sent a message to William at 10:42pm, informing him that an attack was imminent, but that Adriano was refusing to leave.
The attack came at 6:27am the next morning. Harlan managed to escape the safehouse while the other Assassins were killed, and Adriano detonated a bomb to destroy the Assassins' files. Harlan managed to confirm that all of the Templar agents were dead, except for one who managed to escape the blast. Harlan fled to Bologna, Italy, and on 1 December at 12:20pm, Harlan sent a message to William informing him of what happened, and that he was "going dark". William responded by telling him to be strong.
Time in Rotterdam
On 19 December at 9:12pm Harlan was in Vienna, Austria and contacted fellow Assassin Gavin Banks by phone. Harlan confirmed that he was not being followed by the Templars any more and that he was at the safe house. They began to talk about Adriano and how they missed him, with Harlan expressing guilt over leaving him behind. Gavin reassured him that Adriano's death was not his fault and then told him to go to Rotterdam in the Netherlands to await further instructions from him. Harlan then said he would be ready, and Gavin told him to try to relax until then.
In February 2014, Cunningham and his partner Arend Schut, a Dutch MMA wrestler whom he had been training to become an Assassin, infiltrated an Abstergo Industries facility in Rotterdam, where they stole the Precursor box. While making their escape from the facility, they were pursued by Abstergo's Sigma Team led by Juhani Otso Berg. A firefight ensued, in which Cunningham and Schut were able to take down a large part of Sigma Team. They were ultimately forced to leave the artifact behind to make their escape.
Sometime in 2015, Harlan got married to Arend. However, their honeymoon was interrupted by Bishop, who labeled Álvaro Gramática as a high priority target, urging the pair to search for him and his secret laboratory throughout Europe. 
- Cunningham and Schut's relationship was reportedly inspired by the relationship between comic book characters Apollo and Midnighter.