Nathan Johnson is a career criminal, assassin and antihero from the universe designated "Earth-2". He is an alternative universe counterpart of Mr. Sinister and eventually takes up the identity during a later part of his life.
Nathan Johnson was one of many human slaves forced to live under the rulership of a multidimensional alien empire known as the Combine (or Universal Union). He became involved with a mysterious benefactor known as The G-Man, who hired Nathan to assassinate rebellion leader Gordon Freeman and to destroy the leader of the Combine. Nathan soon came into conflict with G-Man, who turned out to actually be using Nathan as a pawn for his own gain. Nathan prevented from G-Man from taking over the Combine for himself, and ended up banishing the alien empire from his reality.
Over the next few years Nathan was involved in many conflicts that came upon earth following the Combine's defeat. Overtime his personality grew darker and he constantly fought with his dark side. Despite killing the "bad guys", Nathan learned that he wasn't doing it as a noble deed, but as a means for him to relish in murder and chaos.
Nathan was elected the leader of the Resistance Government, and led a war against a new invading race of aliens known as the Race X. Shortly after defeating them, he stepped down from the position.
His biggest conflict was with an organisation known as "The Company", who created teleportation and universe jumping technology in a bid to rule the multiverse. During this conflict Nathan's daughter Samantha was murdered by a cult working for the Company.
During his war with the Company, Nathan finds himself in conflict with an alternative universe version of himself by the name of Mr. Sinister, who has crossed over into his reality after striking a deal with the Company. Nathan is drawn to Mr. Sinister's spree of abductions in the Industrial District of his hometown City 17, with the victims being turned into mutated monsters known as "Prowloers" - a new weapon for the Company. Mr. Sinister becomes aware of Nathan's presence and researches him. Mr. Sinister contacts Nathan to meet him on a rooftop in the city, where Nathan sees Mr. Sinister has a daughter similar looking to Samantha (named Sam for short). Mr. Sinister introduces himself to Nathan and explains who he is, and tries to convince him to join the Company. Nathan refuses, and Sinister plans to murder Sam in order to traumatise Nathan a second time. But this plan is foiled when another parallel version of Nathan and Sinister (also named Nathan) sneaks up and attacks Sinister, leading to him falling from the roof and to his death.
After the death of Mr. Sinister, Nathan and the resistance continued their war with the Company, which resulted in the death of their leader Derek Robertson at Nathan's hands. Nathan finally destroyed the Company after killing their true mastermind - a resurrected Gordon Freeman, and afterwards found himself going on the run.
Nathan moves to Steelport to be with his girlfriend Michelle and their daughter Emily. When Cyrus Temple attacks Steelport in an attempt to wipe out the Saints (after framing them for a terrorist attack on a beloved statue), Michelle and Emily are killed in the process and Nathan badly injured, resulting in facial damage. He spends months in hospital, and the trauma snaps his mind and causes him to create a new personality named "Mr. Sinister", based off his alternative universe counterpart he killed a couple of years previously.
- Nathan is an original character who originates from a fan-fiction Half-Life 2 series by the user NathanJohnson, in which he appears as the antihero and one of the main protagonists.
- Like the original Mr. Sinister, this one's appearance is based off Black Mask from the Batman comic books.
- Nathan is a fan of the Saints Row franchise in his own universe.