At the beginning of the series Nathan was a citizen working with the Resistance, before becoming an anti-hero and working with The G-Man, who would later act as Nathan's arch nemesis in the series. Later stories began to depict Nathan in the life of crime and his rise in the criminal underworld, although he had later gone freelance to deal with supernatural and different threats.
Nathan started undergoing a villainous role in the series, and over the course of his time in City 17 developed into a sadistic individual who took a dislike towards humanity. However overtime Nathan began to come out of his self-loathing and cynical nature, and ended up sacrificing his own life in destroying the Clandestine Company.
In an unknown plane of existence outside main time and space, Nathan's fetus was extracted from that of a female abductee from planet earth, which was part of an undisclosed deal she had with a grey-haired man. The fetus was taken to the mysterious man in a blue suit, who had plans for it.
Using alien technology, the fetus was modified to match with G-Man's own will to survive, which he felt would make use for a good agent. During the process, the fetus split into two, which resulted in the creation of Nathan's brother Monty. Monty's development was slow, thus giving him the allusion of being younger than Nathan. Nathan's fetus was matured to three-years-old, and he was taken back to the main universe and to planet earth and observation and slow mental conditioning.
At a facility on earth, three-year-old Nathan was bonded to a woman named Chloe, who acted as his surrogate mother.
At age of eight, Nathan's "family" moved to the Black Mesa Research Facility, where he attended a school there. He developed a crush on fellow classmate Alyx Vance.
At age ten during a school trip to New Haven Zoo, a rival school from Aperture were also attending. There Nathan met Chell Johnson and developed a crush on her.
Nathan and Monty were later put into a combat field at some secure facility in New Mexico, which was observed by the grey-haired man (portraying as their grandfather) and the G-Man. Nathan was shown as efficient in the field despite his young age.
At age eighteen Nathan met Chell once again when he got a job at Aperture Laboratories at a file clerk. The pair of them had intimate sexual intercourse and he impregnated her. Her father Cave Johnson (the CEO of the facility) banished Nathan and had the fetus removed with the help of a personality core, and the fetus was then frozen. Unknown to Cave, G-Man stole the fetus for unknown means. He put in another fetus in its place, which Chell managed to get her hands on and impregnated her with the help of the personality core, which resulted in her giving birth to a baby girl. But this girl wasn't biologically related to her or Nathan, although they would assume this is the case.
Nathan's activities after this, during the Black Mesa Incident and the Seven Hour War is unknown.
Fight against the Combine
After being transferred to City 17 Nathan began working at the City 17 Office. After being attacked by zombies alongside his colleague Billy Bones, Nathan transferred to City 14 where he met another citizen named Samantha Robertson. The pair entered a relationship and got married, however she was killed by her vengeful ex Derrick Thompson in a hit and run, leaving Nathan widowed.
Nathan remained in City 14 to help the Rebel cause there against the Combine and reunited with his younger brother Monty Johnson and also childhood friend Sarah Woods. The trio headed to a Combine base run by a man known as the Consul. The Consul attempted to trap them in a pool filled with Ichthyosaurs, but Nathan managed to launch a grenade at the Consul's control panel which blew him up. They escaped the pool and destroyed the facility and later left the scene, unaware though the Consul had survived.
When Nathan's friend Holly Hills is kidnapped by The G-Man under the orders of administrator Wallace Breen, Nathan returns to City 17 and infiltrates the citadel. But when he accidentally releases Breen's scanner collection, Breen banishes both Nathan and Holly from the citadel, with the novelty of Nathan joining him having worn off.
During the Uprising Nathan and Holly returned to the citadel to deal with Breen. But she was recaptured by G-Man, in order to force Nathan into an alliance as a desperate Breen needed him to stop Gordon Freeman from reaching his office. But Nathan failed and during the destruction of Breen's teleporter at Freeman's hands Nathan found himself flung from the citadel and hit the ground below, causing him to be severally injured. As he died in Holly's arms, Nathan managed to use the F6 key to revert back to his last "save", which was prior to Gordon Freeman's arrival. He then delayed Gordon Freeman's train to City 17, resulting in its destruction being averted. With this result, a new timeline was created.
Employment with G-Man
Nathan returned to the City 17 Office and befriended Simon Simms, Dan Mason and Darko Rascalov. Simon was captured by the G-Man, who wanted to force Nathan to become his new "employee". Nathan grudgingly accepted, and G-Man gave the task of eliminating Gordon Freeman, who in this new timeline has gone rogue and severed ties with G-Man. Nathan spends a couple of weeks tracking Freeman down, before finally confronting him in the City 17 Plaza. Nathan guns down Freeman and shows the body to G-Man, who reveals Nathan has actually killed a body double. The real Freeman then appears and runs Nathan over with his jeep.
After spending a week in a coma, Nathan is reawakened and given another chance by G-Man. During his coma Wallace Breen has been killed after being eaten by bullsquids, but his position of Administrator of City 17 has been given to a man named John Robertson, much to G-Man's annoyance. Wanting the position himself, G-Man hires Nathan to kidnap John's daughter Hannah Robertson so she can be used as a ransom. Nathan carries out the job and takes Hannah to Kleiner's abandoned lab to be held until G-Man obtains the position. The plan works as John steps down as administrator and hands over control of City 17 to G-Man. But G-Man has other plans and plots to kill Hannah. Nathan has a change of heart and tries to plea for Hannah's life. G-Man decides to test Nathan and teleports him many miles away from City 17, and gives him a task to go through a long dangerous journey back to the citadel and see if he will do what it takes to rescue her.
Nathan spends a week battling through the canals, zombie invested Ravenholm, Antlion invested beaches before finally reaching Nova Prospekt. Nathan teleports back to City 17 and makes his way to the citadel. G-Man is surprised and realises he has truly underestimated Nathan's abilities. As Nathan makes his way to G-Man's office, G-Man flees to the teleporter. Nathan saves Hannah and tells her to wait in G-Man's office until he returns, which she nods in agreement.
In the citadel's dark fusion reactor, Nathan and G-Man face off. G-Man pleas with Nathan saying he has made a mistake betraying him, but this falls on death ears and Nathan blasts G-Man with a gun and destroys the portal, which only causes the pair of them to be absorbed in the explosion.
Trapped in the new past
The exploding teleporter sends Nathan back a year to when he first arrived in City 17. Upon awakening on the train, he sees that City 17 is far more grimmer than before. Nathan spends a few months going through similar events that he experienced, although most of it comes down to G-Man. For example the zombie attack he suffered at the City 17 Office now involves G-Men zombies (zombies that resemble G-Men, wearing suits and carrying briefcases). Once the zombie invasion is averted, Nathan decides that he needs to track down G-Man to get to the bottom of what is happening. But he finds himself alone as in this timeline his friends (including Holly) have been imprisoned.
Nathan teams up with Alyx Vance and they track G-Man down to Kleiner's abandoned lab. He reveals he is in control of his alternative universe (which he dubs "G-Man's World") and that he can do anything he wants. G-Man is also shown to have Hannah in his keeping, and plots to finish them off. But while G-Man unveils his plans, Lamar the headcrab attacks him, which gives Nathan enough time to grab an axe and plunge it into G-Man. This results in things being brought back to normal, and Nathan reawakens in present day. Nathan discovers that he has been absent a couple of months, and that the Combine have been truly defeated.
Life of crime
Nathan's actions came to the attention of mob boss Tony Angelo, who decided to employ Nathan as his enforcer. But things didn't go well when G-Man returned to town (now under the name of Frank Blackstone) who wanted back at Nathan for failing him. Frank informed Tony that Nathan was planning to betray him (which wasn't true) which caused a paranoid Tony to try and kill him. But Nathan got the upper hand and shot Tony, but ended up receiving a bullet himself. Nathan faked his death and went on the run to City 16, fearing the repercussions of his actions. But Tony's Underboss Don Simmons took over the family, and he pardoned Nathan as he himself was planning to kill Tony. Monty and Hannah tracked Nathan down to a caravan site near City 16 and told him of the pardon.
Nathan returned to City 17 and reunited with Chell and Samantha. He got a job with the Simmons crime family along with his friends, and became the bodyguard of Don Simmons and also an associate.
Over the coming months Nathan was paired mostly with his friend Dan Mason as they carried out tasks for the family. Nathan also gained influence and got his own small crew and even did jobs with his brother Monty. When Nathan's son Billy Johnson was injured in a fire after Billy tired to burn down his bar to give debts to a loan shark, Nathan had the loan shark beaten and brutally mutilated in prison. This ruthless nature began to concern Chell, who worried for their daughter. Nathan was shown to be more competent in his hits, as he killed rival mob boss Don Gelatray with no problem whatsoever, much a contrast to his early days in City 17 when working for G-Man.
But Nathan and the gang's days were numbered when Don Simmons screwed up on an important deal, which caused a target to be put on them all. Nathan's mentor Andrew Trapani (who was Underboss) betrayed them when he converted to the mysterious Clandestine Company. Nathan left the City 17 Office and went on the run.
It turned out that Dan was an undercover cop and he was willing to let the gang off with their crimes, due to them being friends. Nathan agreed to meet Dan and returned to City 17, but was followed and gunned down by an unknown hitman. Nathan found himself badly injured, but Dan found him and brought Nathan to a doctor for treatment. Nathan decided the best course of action was to fake his death and go into hiding for a while until things cooled down and Dan sorted everything out. Nathan left for City 18 to work for his half brother Jack Clayton and began working as a bodyguard for Nathan's niece Emile Clayton. Back in City 17, Dan managed to have Nathan declared dead and faked a burial.
Five months since his faked death, Nathan resurfaced once things cooled off. He reunited with Chell and chased Frank out of town when he was harassing her and screwed up Frank's chances of running the City 17 Underworld. Nathan and Chell reconciled, but she decided Nathan was unlikely to ever change from his life of violence so left City 17 with Samantha.
Nathan continued to serve his brother Jack but also did some side jobs dealing with crime in City 18. He rescued Hannah Robertson and Vanessa Pade after they were abducted by Toby the Dinosaur, although found out this was tied to a seedy criminal operation plaguing the city.
After Hannah was murdered by Frank, Nathan avenged her death by chasing G-Man to the Xen borderworld and firing a portal at him, absorbing Frank and presumably killing him.
Nathan spent a few months living a peaceful life, although he was tempted to return to his criminal lifestyle as he craved excitement and violence, but chose to put it behind him for the sake of his niece Emile. But his past soon came back to haunt him when Tony Angelo resurfaced after two years and had Emile and her friends held hostage at her school, which was being used as a child factory to make cremator heads. Tony had the place set to blow, but Nathan rescued Emile and her friends on time. Returning her home to Jack, Nathan decided to severe ties with them and vowed to track down Tony and finish him off.
Quest to kill Tony Angelo
Nathan joined an organization named the New Combine - who idolized the long fallen Combine Empire, in the hopes of using them to track Tony down, although Nathan himself was unaware that Tony was actually pulling their strings. Nathan had a change of heart and defected to the Resistance working under Adrian Shephard and gave up what he knew. Nathan raided a building on Gm construct but was required to hold off until Resistance reinforcements arrived to help. Nathan fought off New Combine forces and was eventually saved by the Resistance. Despite their efforts though, the New Combine succeeded in taking over City 17 and put out a Wanted Poster for both Nathan and Adrian.
Nathan traveled to City 19 and began plotting his return to City 17. He was a bodyguard to Adrian's nephew Kyle Shephard, although he got kidnapped which was a ruse to kill Adrian's brother Andy Shephard, who was working with the New Combine, but as part of an undercover operation. Nathan soon realised it was Tony Angelo behind it, and returned to City 17 to stop him.
When Tony was revealed as pulling the strings, he attempted to flee City 17 on a train. But Nathan chased it down with the help of Pyro and they shot at the train and derailed it. Tony survived and Nathan took him back to City 17 and despite being tempted to kill him, turned him over to the authorities instead.
Nathan came to soon regret it. While looking after Holly's sister Paisley Hills, the girl got captured by an escaped Tony and held hostage. She was shot dead by Tony, and in anger Nathan shot Tony in the head, killing him once and for all.
Invasion of the Race X
Not long after the New Combine's attempted takeover, an alien race known simply as Race X began invading City 17 and other parts of Europe. Nathan assisted the Resistance-New Combine allied forces to defeat the aliens and kill their commander Tor.
Troubles with the Russians
Prior to Paisley's demise, Nathan was given a proposition by friend Darko Rascalov to help him out on his drug trafficking business, which will help bring Nathan back on top. But after Paisley's murder at the hands of Angelo, the thought of going back into a life of crime didn't appeal to Nathan and he let Darko down and refused to do his dirty work.
Darko's bloodthirsty cousin Viktor Rascalov convinced Darko that Nathan was a liability, and Darko agreed and decided Nathan needed to die. Nathan got wind of their plans to execute him, and planted a car bomb on Darko's vehicle, causing him to be blown up and killed.
Nathan attempted to reconcile with Chell but found out she had met someone else at Aperture named Doug Rattmann. Nathan was also disappointed to hear that she was planning a new life away with Samantha.
Not long after this Nathan received news that Chell and Doug had died in a motor accident (and by accident their vehicle was blown to bits). Nathan mourned for Chell, but decided to start taking responsibility for his daughter and planned to go straight. Nathan cut off his past ties to organized crime and began taking up more legit work in order to support his daughter.
The last battle
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. They then return to City 17 and celebrate their victory with a party.
Shortly afterwards, Nathan and Samantha leave City 17 together for a new life.
Working for the Company
Some years later Nathan returned to a rebuilt City 17 and began working as an IT analyst at a corporation nicknamed "The Company". There he befriended Olivia Harris, whom he had met during the Combine occupation many years previously. By this point Nathan had been married (but widowed) and has a seven year old daughter named Samantha.
Investigating a secret society
Nathan was made aware of the inner workings of a secret organization named the "Clandestine Company" when his friend John Robertson phoned him for help. Nathan headed to John's apartment, only to find it has been cordoned off by police, and Nathan was told by Agent Dan Mason that John was found dead.
Nathan entered the crime scene once police had left, and discovered symbols scrawled on the walls. He took some photos and returned to his apartment, and found an email sent by John prior to his demise, with the words "Call of Clandestine".
A couple of weeks later, Nathan and Samantha were attacked at their apartment by a mysterious figure, but were saved when an agent named Thomas Wilson burst in and shot the man down. A few days after this incident when Nathan was waiting by the bus stop, he was approached by a disguised Thomas, who told him the Clandestine Company were a secret society running everything from behind the scenes, and should watch out. Thomas then disappeared.
Back to Black Mesa
Nathan's post City 17 life would be all happiness when a vengeful Viktor captured Samantha and ended up going back to Black Mesa, just prior to the Black Mesa Incident. Teaming up with Alyx Vance they used Isaac Kleiner's teleporter to travel back in time. Viktor unveiled his plans to Nathan, that he will be manipulating the incident for his own gain and will be sending Nihilanth's alien race to present day earth. Nathan managed to save Samantha and sent her and Alyx back to the future, meanwhile Nathan headed to the Xen Borderworld to stop Viktor's plans.
Nathan teamed up with Gordon Freeman and arrived at the Nihilanth's lair. Viktor was betrayed by the creature, who killed Viktor and prepared to launch its Xenian fleet to modern day earth as part of it's new invasion. Realising this could have an awful effect on reality, Nathan and Gordon teamed up and fought against the Nihilanth, eventually destroying it. As Nihilanth exploded, a new reality was created when the rift in the dimensions closed, thus preventing the Combine getting through (unlike the original timeline). Nathan then found himself returned to a modern, yet different, world.
Nathan awoke in modern day 2014, but in an alternative timeline in which the Combine weren't in control. Here he was living in a town named New Haven, located nearby the newly rebuilt Black Mesa Research Facility, and with his wife Samantha Robertson (who is alive in this timeline) and their son Gareth.
Nathan managed to return to his original timeline.
The following year
After returning to his original timeline, Nathan knew he hadn't seen the last of his enemies, especially Wallace Breen. Knowing the existence of alternative timelines and that any of his foes could return, Nathan sent his daughter Samantha away to live with relatives and even changed her hair colour from blonde to brown and even had her name changed as he didn't want to risk anything terrible happening to her. Nathan gave up his life of crime and violence and instead settled working in a fish restaurant washing dishes and keeping his head down. Nathan decided to make most of this normal "boring" situation, knowing that it won't last forever.
Nathan spent the next year working in the restaurant doing his dish washing and began living a shabby life and wasn't taking care of himself properly. A calling came when his grandfather Consul contacted him from a hospital wanting Nathan to meet him. Along with Sarah they went to the hospital and visited Consul, who told Nathan that the Clandestine Company were returning.
The Path to Clandestine
Nathan regrouped with his old friends in order to work against the Clandestine Company after learning of their upcoming plans of world domination. During this, Nathan ended up infected with the C-Virus which caused him to turn really old and worn out. Thanks to a group known as the Elders Clan, he fought the disease and returned back to normal.
Nathan owed a favor to the Elders Clan, and was forcefully made into a warrior titled the Elder's Knight. His task was to infiltrate the Evo Corporation and steal the C-Virus formula. Nathan did so under partial brainwashing and fought CEO David Wakeham, who had been converted into the Cyber Gimp (similar to Jim Darwin). After killing Wakeman (who gave Nathan some cryptic information on the Clandestine Company) he stole the vat of C-Virus formula. The Elder Leader attempted to betray Nathan, but foreseeing this Nathan gassed the Leader, causing him to rapidly turn old and die from advanced aging.
Thanks to information from Frank Blackstone, Nathan learned the first phase of the Clandestine Company's invasion was the 18th May 2016, and the second phase titled "Endgame Protocol" taking place on 22nd August 2016 (and coincidentally, ten years since Nathan arrived in City 17). Nathan tried to obtain information on exactly what would happen during the first phase.
The populace's health began to deteriorate, and Nathan saw it was the sign of the C-Virus and realised the Company must have had a vat left. But he and his friends weren't affected. City 17 then came under attack by Clandestine Forces, and portals began opening which allowed through demons and monsters, and assorted aliens such as rogue Xenians and Race X soldiers. Nathan, and his friends Dan Mason, Simon Simms and Don Simmons managed to escape City 17 and get past the barricade, before it was completely taken over and locked down.
Defeating the Company
Nathan confronted Derek Robertson at the Nexus Building and demanded he stopped the invasion. But Nathan began to succumb to the C-Virus which was still lingering in his system. As he started to breakdown, Derek goaded him for his failure. However Nathan told Derek that even though the Company were victorious for now, he will never be able to witness it, and with that subsequently shot Derek in the head and killed him instantly. Nathan then vacated the city.
Nathan reunited with Chell and took in his niece Emile Clayton. They moved to City 14 where they settled down, feeling the Clandestine Company would be at a loss without Derek. But unknown to Nathan, it was all far from over.
The G-Man leaks information to a mysterious individual named The Dark One - who is the true leader of the Clandestine Company. Emile is kidnapped and Chell is injured. When Clandestine Agents attack City 14, Nathan manages to escape and heads for City 17.
Nathan reaches the citadel and plans to stop the Dark One's incursion. He is captured and taken to Wallace Breen's old office where the Dark One unveils himself as Gordon Freeman. Freeman reveals his contempt for humanity and that he was simply being used. Freeman makes an ultimatum to Nathan to join him as his second-in-command, as he is planning on opening a portal to a mysterious dimension to let through a new alien race. Despite feeling the same as Freeman, Nathan decides not to fall to his darker side again and refuses. Freeman becomes frustrated and plans to execute Nathan, but Chell and Alyx Vance gain access to the office and save Nathan. Freeman makes a run for it and heads for the citadel's dark fusion reactor with the intent to open the portal.
While Alyx and Chell go to save the prisoners which include Emile, Nathan faces off with Freeman at the portal. Freeman starts the countdown sequence and the pair of them end up involved in a brawl. Nathan stabs Freeman in the leg and the chest, killing him. He takes Freeman's access code and heads back to Breen's office where he regroups with Alyx and Chell who have just evacuated the prisoners. But it turns out Freeman has made sure the portal opening will go ahead. Nathan makes the decision to destroy the portal, and after saying he loves Chell teleports both her and Alyx away using his portal gun. Nathan then activates the self destruct sequence and sits back and waits for the top of the citadel to be destroyed. He is visited by an apparition of his daughter Samantha, he stays by her father just as the portal is destroyed and Nathan is thrown from the citadel and killed. The destruction of the citadel also brought down the Clandestine Company's resources and most of their followers, thus ending them.
Although Nathan's body isn't found, he is still given a burial at Ravenholm Cementary. Chell and Emile visit his grave.
Serving the Elders
In reality, Nathan again survived another near death, which was thanks to the intervention of the Elders. The Elder Supreme had Nathan placed into stasis, saying he would be awoken when the time was right.
After some time had passed, Nathan was awoken by the Elder Supreme on a mission to take down Toby Purnell, who had managed to breach the gates of the universe causing issues with time and space. Toby had began residing in the "real world", in which their existence was brought about by a video game series and fan-fiction. Toby plotted to use this knowledge to bend and shape their reality to his own image. Nathan was sent to this universe, where he took possession of his creator Callum Harper - who had been executed by Toby.
In the possession of Harper, Nathan united with the real life counterparts of his gang: Dan Mason, Simon Simms and Don Simmons, in order to track down and defeat Toby. Toby surrendered to Nathan, as he had been betrayed by his right-hand-man, who he himself planned to rule the multiverse. Nathan managed to stop the man by using the same reality bending abilities of the G-Man, and flung him into a hellish dimension known as the "Horror verse". Nathan handed Toby over to the Elder Supreme, and was allowed back to his City 17 universe, although the Elder told Nathan he maybe called upon again for his services. Nathan was shown to have a portal and dimensional bending device known as the "Displacement Cannon", which he pondered to use to jump back to the real dimension and start a new life.
Due to the intervention of an unknown party, Nathan found himself reborn in a brand new universe which was a composite of the broken City 17 Universe and that of the real world, and that years of his life had been shed off as it did in that reality.
Nathan awoke, with memories intact, in a period shortly following the downfall of Wallace Breen. In this new universe, a woman named Jackie Robertson (a female version of the late John Robertson) was in charge of City 17, and that Hannah Robertson was her daughter and alive and well.
In this universe, Nathan has been involved in the past with Jackie, although he has no memory on the extent of their acquaintance. Jackie trusts Nathan to take care of Hannah, although this ultimately fails when Hannah is abducted by a man posing as Nathan. Nathan suffers déjà vu due to experiencing a similar incident many years prior, and believes his archenemy The G-Man is again responsible. However it turns out to be Wallace Breen's older brother, nicknamed "the Administrator", who like G-Man in the original timeline wants Wallace Breen's power. Nathan rescues Hannah, and the Administrator is placed in prison.
- Note: The following information is non-canon to the main series
City 17 Street Redux
- See article: Mad Hatter
In an alternative timeline in which Nathan took over the Clandestine Company and allowed their multi-dimensional invasion, he became their supreme ruler known as The Overseer. Nathan's personality darkened greatly, and he became a cold, calculating and remorseless, although he claimed he was doing what he was for the good of the human race and alien allies.
Nathan set up his base of operations in City 17, due to being in love with the city, and had his mysterious alien allies set up alien spirals across the city.
Nathan went into partnership with Chell, however upon finding out she was planning to assassinate him had her imprisoned at the newly built Nova Prospekt in City 17, where he sentenced her to life. He placed their adoptive daughter Emile in a Combine reform programme to have her turned into a drone.
- Monty Johnson — Brother
- Darren Johnson – Son
- Billy Johnson – Son
- Samantha Johnson — Daughter (Deceased)
- Hannah Johnson – Daughter
- Samantha Robertson — Wife (Deceased)
- Susanne Johnson — Mother
- Consul — Grandfather (Deceased)
- Jack Clayton — Half brother
- Emile Clayton — Niece (Deceased)
- Monty Johnson - Brother
Personality and skills
Nathan seems to have different mood types depending on his situation. At times he comes across jokey, but sometimes quite sadistic and murderous.
Upon his original arrival in City 17, Nathan came across quite meek and almost wimpish and almost didn't seem phased by how far humanity had come down due to the Combine. When around his first wife Samantha Robertson he came across almost like a clown and immature in his behaviour.
After her death Nathan still retained his more jokey and immature behaviour, but started developing a more serious side to him. He also showed a protective side, especially when it came to Holly Hills and his friend Simon Simms. This part of him would stay intact even during his more darker turn down the line.
Nathan displayed himself as a bit of a pushover and easily talked round, and took orders from Frank Blackstone to do several tasks. Even in his earlier days in City 17 Nathan had skills such as weapons use and also being able to survive dangerous situations.
In the aftermath of the Combine's downfall and the subsequent years Nathan's mood became darker and more cynical and he found himself in conflict with his feelings. Although wanting to be a good guy and settle down, he still longed for danger and carrying out criminal tasks. Although still protective of his loved ones, Nathan still put his work before them.
With every passing disaster and loss Nathan's mood fouled more and more, and his more joyful and clownish persona began to fade. In order to deal with this he had a secret split personality which took the form of Frank Blackstone, which retained his more evil personality. Nathan would get into conflict with this secondary persona, but eventually accepted it was a part of him and the only way to cope.
During the Clandestine Company's slow-burning takeover of City 17, Nathan was in even more of a conflict with his thoughts. Although working to destroy them, a part of him wanted to accept their dark agenda. As it turned out, their true leader Gordon Freeman (Nathan's old 'archenemy') banked on Nathan finally accepting his darker side and joining him. During the Clandestine Company's final phase of their takeover, Nathan came close to deciding to join Freeman's cause in purging humanity to be replaced with a new superior alien race, but snapped out of it and opposed Nathan's plans. After years of conflict and terrible deeds, Nathan chose to redeem himself and destroy Freeman's portal to prevent the aliens coming through, but at the expense of his own life.
- Nathan uses the Male_07 model from Half-Life 2 with different variations.
- Nathan was originally introduced as a minor character when City 17 Street began. He was credited as "Citizen" in the "Pilot", before being named for the first time in "Another Day". The character was promoted as the main protagonist in "Pool of Death".
- Some episodes give Nathan's whereabouts during the events of Half-Life 2 and his brief encounters with Gordon Freeman. In "Pilot" (before a flashback set before Half-Life 2) Nathan is meant to be the Male_07 citizen on the same train which Freeman boards City 17 on. A later episode (which crosses into the original events of Half-Life 2) shows that Freeman threw a can at his head during Chapter 1 Point Insertion (which is something the player can do to a citizen). He then later witnesses Freeman blowing up the dark fusion reactor and presumably killing Wallace Breen during the final chapter of the game, although Nathan somehow prevents these events by time traveling and creating an alternative timeline.
- As such his apartment is the same one that Freeman first enters in Point Insertion when cops are raiding the place.