- "I'm sorry. I didn't realize you wanted him to shoot you. I can call in some more guards if you like.
- —Jonathan Steinberg
Jonathan is first introduced at the end of Mission 7 when he saves Joanna from Chandra Sekhar. He explains that he and his squad were sent there to save her, download Zeigler's program and destroy the Trinity Base. After they're extracted from the base, he remarks on how good Joanna's combat skills are and how they "made a good team back there". He then introduces Joanna to Daniel Carrington via hologram, who in turn convinces her to team up with the Carrington Institute - for the time being.
Later on while in Peru, Jonathan and his squad are captured by dataDyne and are brought to Africa for interrogation and execution. After Joanna saves them, he and his squad provide support for her through out the rest of the mission.
In the beginning of Mission 12, Jonathan is in a hovercraft that is blown up by dataDyne jetpack troops. He survives the explosion, but due to his injuries, he is unable to provide adequate support for Joanna. Joanna then escorts him to the bridge where Carrington and several Institute members are stationed.
At the end of the game, Jonathan - despite his injuries - leads a squad to the Colosseum where Joanna was last. When the arena Joanna and Zhang Li were fighting in collapses, Jonathan signals his squad to not fire upon Joanna. Jonathan staggers forward to help Joanna as she collapses due to her own injuries. He helps her up as Carrington arrives to talk to her. As the game ends, Jonathan can be seen wrapping his arm around Joanna's shoulders.
Jonathan is sent to Area 51 by the Carrington Institute to spy on the NSA. Carrington's "friends" - the Maian delegation - are shot down in Nevada and the equipment, bodies and survivors are recovered by the NSA and taken to Area 51 for studies. Jonathan manages to get a video out to the CI, who send Joanna Dark to assist him in the rescue of any survivors.
Joanna meets up with Jonathan who helps get her further into the facility by providing her with explosives. Joanna manages to rescue the comatose Maian Elvis and hides him in a safe place. She locates a Maian medkit and meets up with Jonathan again; they fight their way back to Elvis and revive him. However, their immediate escape is thwarted - there is only room for one passenger on board Elvis' flying saucer, and someone will have to stay behind and open the hangar doors so that it may leave.
If Joanna chooses to flee with Elvis in his spacecraft, Jonathan succeeds in opening the hangar doors, but is assumed to be killed trying to escape the base himself as he is absent from the rest of the game. If Joanna orders Jonathan to take her place aboard the saucer, her own escape will be made more difficult, but Jonathan will survive the mission.
If Joanna chooses to assume responsibility for opening the Area 51 hangar doors herself, Jonathan will reappear during the Skedar assault on the Carrington Institute headquarters, where he covers Joanna's back as she breaks into Carrington's safe and destroys the sensitive data stored within. It is again possible for Jonathan to be killed, although in this instance there is little Joanna can do to impact his chances of survival.
Jonathan's canonical fate is unknown, as he is never seen again in the game even if he survives the Carrington Institute attack, and his death will not result in a mission failure.
- In the 'Duel' mission in Perfect Dark on the Special Agent difficulty, it tells you to assassinate Jonathan Dark, revealing he is Joanna's brother. Also, the co-op character, Velvet Dark is Joanna's sister. In Perfect Dark Zero, Jonathan Dark is renamed Jonathan Steinberg, retconned to have no previous relationship to Joanna Dark.
- The only time when Jonathan is a playable character during co-op in Perfect Dark Zero is during Mission 8. The rest of the time the co-op partner is either Chandra, Jack Dark, or a generic Carrington Institute member.