In Under Control, John comes back to Mystic falls where he was warmly greeted by Mayor Richard Lockwood and the other members of the founder's council. However, he knew much more than them, including that the tomb vampires had been released and he was secretly planning to eliminate them all.
When he and Damon met, they talked a little. John told Damon he knew what he was. He knew that Stefan Salvatore and Damon Salvatore are vampires.
He blackmailed Damon with the knowledge of his secret, trying to get him to help finding a piece of Johnathan Gilbert's invention. The device emits a noise on a certain frequency that is harmless to humans but renders vampires totally helpless by a deafening sound. Damon knew he was on vervain so he broke his neck and threw him down thinking he was dead. He didn't know that John came back to life. When he came back to life he walked past Damon who was surprised and joined the mayor ringing the bell so he did that's when Damon saw his ring. Damon figured out that John and Alaric had the similar rings that prevented the bearer from dying from any supernatural cause. When John walked outside, Damon and Alaric joined him, wondering aloud how he knew so much about everything. He then asked, "How do I know anything Damon?" and walked away.
In Founder's Day, John began to prepare his plan with Johnathan Gilbert's invention to neutralize the 1864 tomb Vampires. He and Mayor Lockwood agreed. But Sheriff Forbes did not agree due to the danger it poses to the innocent citizens, prompting John to knock her out and cuff her hands so he can go on with his plans.
He then continues his plan by activating the Gilbert Device. But before he does, Damon warned him that it won't work. Damon did not know that Bonnie actually did not de-spell the device, so it still actually works. Every vampire within a 5-block radius hears the sound from the device and they are crippled by its defeaning noise, rendering them weak. The police then move on to inject vervain on everyone who fell down and were affected by the noise. This included Mayor Lockwood because the device actually affects werevolves as well. Tyler Lockwood is also affected but he is driving away from town and was not injected with vervain or thrown into the building with fire.
They placed all the vampired in an old house which the Gilberts own and took them into the basement. John starts putting oil over the vampires in order to light a fire and burn them to death. Anna and Damon wake up. John goes over to Anna, recognizing her. Anna puts her hand on John, but he stakes her and she dies as Damon watches it happen, also weakened by the vervain.
John returned to Mystic Falls in The Descent. When Damon found out Stefan had brought back John Gilbert he was angry, commenting how john tried to "barbeque" him. Later, Damon looked for John to talk to him. He sees Elena and asks her if John was home. Elena tried to calm him down, asking him not to kill John. Damon says he was just joking but says he might be serious, too. Damon and Elena then go out together and find John at The Grill talking to Jenna Sommers and Alaric Saltzman.
Damon approached John and asked him about what he knew. John told Damon he knew about The Sacrifice and The Originals but he didn't trust Damon enough to tell him more. "First, I need to know if I can trust you Damon, and that I can count on you. Then, we talk."When Damon and Elena are arguing about how Werewolves should die, John comes and ask what is going on. Both of them say nothing but he doses`t believe that. Then Damon says, "Well it's a two way street John. Now get out." Damon then goes but lets John make sure his daughter doesn't go anywhere near danger.
It's night and someone is knocking on the door at The Salvatore Boarding House, and when Damon opens it, he sees John Gilbert. He was wonders why he was here and John tells him they weren't done with their earlier conversation. John then shows Damon something - something that can kill an Original Vampire: a Dagger with The white oak ash. Together, it can kill any Original Vampire. He then goes and leaves Damon to kill Elijah, but something he didn't tell Damon was that if he kills Elijah then both of them dies.In The Dinner Party, John comes to The Salvatore Boarding House since he heard that Jenna was coming to a Dinner Party witch Elijah coming to. When John came they where all surprised and Jenna aks "Who Invited him" and Damon says "John, leave" and John says he will join them at The Dinner Party. When The Dinner party starts John is listening to an old Witch story Elijah is telling about The Witches who lived In Salem. In The 16th Century. John Says to Elijah "It sounded kinda, like a ghost story to me." When Damon is about to kill Elijah with The white oak ash Dagger, Alaric interrupt and write on a paper that if you use The Dagger it will kill both of you. When Damon comes back he looks at John and John looks at Damon, He says to Elijah "You know that John is Elena`s uncle/father, and of course she hates him. "So there is no reason to keep on the endangered species list." Then Elijah is killed by Alaric With The White Oak Ash Dagger. After The Dinner party John and Alaric talks and John says "You know I can clear all this about Isobel if you want or Not." But Alaric says "You want it take it. And after what you did to Damon you`re gonna need it more then me."
In The House Guest, Katherine Pierce reveals to Damon Salvatore that she and John Gilbert made a deal, she help kill Klaus or He would kill Stefan, But she had to choose witch of The Salvatore Brothers should Die or Live.
In Know Thy Enemy, Isobel returns and everybody is curios why she is back except for John Gilbert, When Isobel kills John, Katherine captures Elena and gives her to Isobel. When Damon comes to The Lockwood Mansion he sees that John has his Gilbert ring and explains it to Carol Lockwood and Liz Forbes that he is okay and will be alive soon. Damon takes John to The Salvatore Boarding House and drops him at the floor and washes away John`s blood fom his hands and clothes. When John wakes up Damon goes to him and is holding him up but Elena says to let him go.
John: We didn’t get the chance to meet at the council meeting.
Damon: Yeah. That’s a pleasure. Are you enjoying the kick-off?
John: Oh yeah. I forgot how much fun these small town celebrations can be.
Damon: Yeah. When was the last time you were here?
John: Hasn’t been that long, my brother’s funeral. How long have you been in town?
Damon: Well, not long at all.
John: So what do you think Damon? You know this vampire problem is real right? It’s a potential blood bath
Damon: I would not overreact John.
John: Oh, I think it’s like 1864 all over again, vampires running a mock. I guess we just gonna have to hunt them down, throw them in a church and burn them to ache.
Damon: This is the story hein?
John: Part of the story, yeah
Damon: Oh, there’s more?
John: Oh there’s lot more. See, it seems there was a tomb under the church, where vampires were hidden, waiting for someone to come along and set them free. But you already knew that didn’t you?
(Damon doesn’t look at him. He’s uncomfortable.)
John: Because you’re the one that did it.
Damon: And you’re telling me this why?
John: I just thought we get the introduction out of the way.
Damon: You know that I could rip your throat out before anyone would notice?
Damon: Yeah, okay. But you probably ingested vervain so…
John: Why don’t you take a bite to find out?
Damon (smiling): This not worth my time.
(They look at each other and smile. Damon leaves but he rushes on John with his power. He breaks John’s neck and throws him over the balcony. He smiles and leaves.)
-- Under Control.
(John is lighting a candle for the victims. Damon rejoins him.)
Damon: So John, rumor has it that you know a lot and won’t say anything.
John: How can I know you can be trusted, Damon? Originals can compel vampires and according to Stefan, that’s why Katherine’s still in the tomb, because an original has compelled her to stay there.
Damon: Only because all of the vervain have left her system. Stefan and I on the other hand are chock full.
John: You guys are drinking vervain?
Damon: It’s an acquired taste. I don’t see that magic little ring on that stitched finger so if you know something about Klaus, you better start talking or I will kill you in your sleep. John: Is that any way to convince me that you and I are on the same side? First, I need to know that I can trust you, Damon, that I can count on you. Then we’ll talk.
-- Daddy Issues.