When John was young he used to date Isobel Flemming who was an descendant of Katherine Pierce, a vampire and the first Petrova Doppelgänger. Later, John discovered she was pregnant and he took her to his older brother Grayson Gilbert who was a doctor who helped deliver the baby girl. After giving birth, Isobel fled leaving their daughter, Elena, with the Gilberts. John also left Elena, who is the second Petrova doppelgänger, with Miranda and Grayson. Elena had been raised by them, as if she was actually their daughter. In a car accident, Miranda and Grayson died, but Elena, who was in the back seat of the car, was saved by Stefan Salvatore at the request of Grayson who was the only one still conscious. He made Stefan get Elena out before he would accept help himself. When Stefan returns to the car to help Grayson and Miranda however, they were already dead. Grayson and Miranda's deaths hurt Elena a lot, seeing as they brought her up and she believed them to be her birth parents.
In a conversation with Matt Donovan, Elena reveals that she never really liked John whom she believes to be her uncle. Elena is hurt and angry when she finds out she is adopted, and in complete shock when Stefan tells her that John might be her father in the season finale. Later, when trying to save Damon Salvatore from a burning building, she confronts John, saying that "as her father" he should care about how she feels for Stefan. John doesn't seem very surprised that Elena knows of their real biological relation, but still lets her pass to save Damon. After John is stabbed by Katherine, Elena returns home to find him lying on the floor bleeding. She comforts him, telling him everything will be alright.
Season 2EditJohn appears more often with an agenda which is to help Elena, to which she replies that she does not want him there and he should leave Mystic Falls. Isobel later returns and John, invited back home by Stefan, invites her into the house, making it harder for Elena to trust him. Later, after Elena witnesses Isobel's death by sunlight, John tells Elena that, despite Isobel's cold demeanor, she truly did care for Elena and was upset to leave her with Grayson and Miranda. John gives Elena the option on whether she wants him in her life anymore, saying he will leave her alone if she asks him to. Though Elena points out John's negative traits, she decides to give him a chance, since he is the only parent she has left. They stay in touch afterwards. When Elena is sacrificed in Klaus' ritual, John makes a sacrifice himself. He gets Bonnie Bennett to cast a spell, linking his life-force with Elena's so she won't become a vampire due to Damon's blood being in her system. Jeremy Gilbert asked John if he knew what the consequences of his sacrifice would be, and John said he did. The spell worked and Elena was brought back as a human, but to keep the balance of nature correct, John himself died as a result of the spell. It shows that even if Elena has trouble trusting John, he loves her and is willing to give his life to save hers. He leaves Elena his Gilbert ring for any children she may have in the future; as she is a supernatural occurrence, the Petrova doppelgänger, the ring will not work on her herself, and also a letter which says that he would have loved her as a human or as what he hated the most in the world, a vampire, because she is his daughter.
- It's no easy task being an ordinary parent to an extraordinary child. I have failed in that task. And because of my prejudices, I've failed you. I'm haunted by how things may have played out differently, if I'd been more willing to hear your side of things. For me, it's the end. For you, a chance to grow old and someday do better with your own child than I did with mine. It's for that child I give you my ring.
- I don't ask for your forgiveness or for you to forget. I ask only that you'll believe this: Whether you are now reading this as a human or as a vampire, I love you all the same, as I have always loved you and always will.
John's funeral is attended by the two surviving members of the Gilbert family, Elena and Jeremy, and also by Alaric Saltzman, Stefan, Damon, Caroline Forbes, and Bonnie. Elena lays a single red rose on his grave, as well as one on Jenna's grave and two more by the gravestone for Grayson and Miranda.
- For most of Elena's life she thought John was her uncle. Grayson and Miranda were unaware of Elena's biological father.
- At the end of Season Two, Elena and John end their relationship on good terms as he dies so she will not become a vampire.
- In Stand by Me, Elena admits she misses John, something she herself is surprised by.