Samantha Johnson is the daughter of Nathan Johnson and Chell. She was born in 2004 at Aperture Laboratories, and in 2008 moved to City 17 with her mother after the fall of the Combine. When Chell died in 2014, Samantha stayed with her father full time.
Samantha was conceived at Aperture Laboratories by Chell and Nathan Johnson. GLaDOS had hoped to use the child as a possible future subject, but Chell rescued her daughter after defeating GLaDOS and escaping Aperture.
In July 2010 six-year old Samantha arrived in City 17 with her mother after they got report that Nathan was dead. However Nathan had only faked his death after killing mob boss Tony Angelo and when he was pardoned by Tony's successor Don Simmons did he finally reunite with Samantha and Chell, whom came to stay with him.
In December 2011 Chell left City 17 and took Samantha with her, although the pair of them continued to visit Nathan, especially for Samantha's birthday and around the Christmas period.
On Christmas Eve 2013, Samantha was kidnapped by Viktor Rascalov as a way to stop her older brother Darren Johnson from taking down his criminal empire. But Darren managed to rescue Samantha and defeat Viktor.
Following the death of Chell, Nathan plans to leave City 17 with his daughter Samantha and become a better father and put his life of violence behind him. But Samantha is abducted by a Combine Prowler and Nathan receives a message from Wallace Breen (who has been presumed dead since the Combine's downfall) that he has her and orders Nathan to come to the citadel.
Nathan obliges but is knocked out and placed in a stalker pod. He is taken to Breen's old office, where Breen himself and The G-Man await. They tell Nathan that they plan to destroy City 17 and plan the rise of a new Combine Empire, and will be using Samantha as their employee and assassin, due to the fact Nathan had failed them in that regard. They show Samantha to Nathan, and she is taken away to their escape pod by a brainwashed Gordon Freeman. Breen and G-Man bid farewell before departing, leaving Nathan trapped in his pod and at the mercy of Breen's men. But Nathan's friends Simon Simms and Dan Mason arrive to save him and kill Breen's men before they can administer torture on him. They track where Breen's pod is heading and find it is going to a castle many miles out in the countryside and away from City 17. Nathan enters another escape pod, while his friends stay behind to keep the core stable and prevent destruction.
Arriving at Breen's castle, Nathan dons a Combine outfit and manages to access the place. He is soon detected however, but manages to shoot through Breen's troops. Nathan tracks Samantha down in a dungeon and rescues her. Nathan comes face to face with G-Man but manages to overpower and knock him out. Breen tries to escape, but Nathan confronts him on top of the castle and shoots him, which causes Breen to fall off the edge. Nathan hacks into a computer and manages to prevent City 17 from being destroyed. He then wires the castle to self destruct, and escapes with Samantha and a captured G-Man in Breen's escape pod just as the facility is destroyed.
A couple of weeks later Samantha and Nathan leave City 17 for a new life.
Sixteen months since leaving City 17, Nathan left Samantha to stay with his close friend Sarah Woods whilst he went on a mission to an alternative universe. By this point Nathan had become paranoid of the Clandestine Company coming after Samantha, so had her hair dyed brown in order to help conceal her identity. Regardless though, she was kidnapped and sacrificed by a Cult working for the Company.
When Nathan was infected with a specialised virus known as the "C-Virus", he began fighting against the contagion. In a dream like state, he protected Samantha from a monster like creature. After defeating the monster, Samantha's flittered away, and Nathan seemed to move on from her death.
In the grand finale of City 17 Street, Nathan must come to a decision to either destroy the citadel, thus preventing Gordon Freeman's super-portal from allowing a new, rogue alien race to come through and invade earth, or let the plan commence. In the primary (and canon) ending, Nathan decides to self-destruct the citadel and kill himself. Just prior to detonation, he is visited by Samantha's apparition, who tells him it will be alright. He holds her close, and accepts his demise and feels at peace.
- She uses the child worker model from the Half-Life 2 beta, but with modified long blonde hair and blue eyes. However earlier appearances depicted her with the vanilla model, which showed her with brown hair and brown eyes.