- "He's a good guy, though. He's just... he's a lot to take sometimes. All that he's been through. You know... what are you supposed to say to that?"
- - John Connor.
John and Derek's friendship is one of the most complex on the show. In the future, an older John is the leader of the Resistance and Derek's commanding officer. In the present, Derek is John's mentor and uncle.
Upon first meeting him, John cared very little for Derek, despite him being a Resistance fighter sent back by his future self. When Derek is shot and Sarah expresses her desire to kidnap a doctor to save him, John angrily opposes this move, calling it "crazy, even for you". When he learns that Derek is his uncle, however, John immediately rushes to find Charley Dixon and brings him back to the house so that he can save Derek. As Charley works on an unconscious Derek, John paces anxiously in the other room, hoping that his uncle survives. He later volunteers to donate a large amount of blood to Derek and remains by his side throughout most of the day, eventually telling him the story of Kyle's death.
While Derek recovers, John expresses his desire to keep him close and hopes that he will live with them, calling him "family". They find themselves at odds, however, as Derek openly opposes Cameron's presence and questions John's trust in her. When Derek accuses Cameron of treachery, John takes her side as opposed to his uncle's and adamantly defends her from his damning accusations. In "What He Beheld", John is shocked by Derek's ruthless efficiency when he is held captive by the Fake Sarkissian. Derek likewise holds a little girl hostage in a bid to convince the man to let John go. When this fails, Derek shoots the man in the head, despite the danger of hitting John in the process.
Despite being rattled by his behavior, John and Derek later bond when the latter reveals his knowledge of their relation by taking John to see his 5 year-old father. They are once again put at odds, however, as Derek later tries to convince John to destroy an unstable Cameron. When John risks reactivating her, Derek tries to rush in and stop him but is held at gun point by his nephew and looks on darkly as Cameron takes her place by John's side. In "Goodbye to All That", they both decide to infiltrate a military academy in order to protect a Skynet target from termination. During this mission, John has an opportunity to understand his uncle's mindset as a traumatized soldier and learns the level of self-sacrifice that Derek represents.
In latter episodes, he is starting to show concern for John, who is suffering from post-traumatic stress from killing Sarkissian, though Derek does not know his nephew was the one who killed him. Derek later grows frustrated in John's reluctance to step up to his destiny, stating that "that boy is becoming less like John Connor and more like John Baum every day." In "Strange Things Happen at the One Two Point" Derek confronts John and asks him if he is seeing straight in regards to their mission, which angers him, as he believes Derek to be questioning his integrity.
- John and Derek only ever argue about Cameron and her loyalties. Aside from this, they get along well enough.