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- "While humanity is your greatest strength, it is also your greatest vulnerability." – Martian Manhunter, to Clark, Bizarro
The relationship between Clark Kent and John Jones began when John Jones assisted Clark in stopping a Phantom Zone escapee, Aldar. They both share a unique relationship as both are aliens that reside on Earth because their civilizations were destroyed as well as John knowing Kal-El's Kryptonian father, Jor-El.
Clark's first encounter with the Martian Manhunter was when he went to Seattle to find Aldar, an escapee from the Phantom Zone. Just as Aldar was about to kill him, he fell down dead in agony and Clark was shocked to see a handprint on the Zoner's back, then he saw someone super speed away. As Clark pursued him, he stepped on an Oreo cookie. He chased him onto the dock and when the stranger turned to face him, his eyes glowed. Then he took flight, leaving a red streak behind him. When Clark returned to Smallville, he found another Oreo cookie in his loft. When Chloe arrived, Clark told her the crystal hadn't worked but someone else with powers greater than his had saved him.
When Clark was attacked by Dr. Hudson, another Zoner, he was caused to believe that he was a mental patient with no superpowers. Another patient however, told him that he was from Mars and that he believed him. When Clark woke up from his delusion, he saw the other "patient" mysteriously standing over him, holding a crystal that captured the phantom.
After Clark discovered that Lionel Luthor was the reason Lana went through with her marriage to Lex by threatening his life, he attempted to kill him but he was stopped by the Martian Manhunter, who revealed he was working with Lionel to find the last wraith from the Phantom Zone. Clark realized that he had come into contact with the last wraith and the Martian urged him to find it.
It is not clear whether the Martian Manhunter had been hunting the Zoners indivdually or simply stepped in due the extreme threat the last phantom had poted to Clark.
- "Losing Lana has made me realize no matter how close I get, someday they'll all be gone. And all the time I've spent ignoring my destiny, trying to be something I'll never be: human." - Clark Kent to Martian Manhunter, Bizarro
Clark later called out for John's assitance in his continuing battle against Bizarro, after he returned to the Earth's atmosphere from healing from a wound. John explained to Clark that Bizarro was discarded as a poor imitation upon creation and shown no compassion, and therefore he had none. Clark talked of how kryptonite made Bizarro stronger and when his face changed when he stepped into the sunlight. John gave him a clue on how to defeat Bizarro and urged Clark to fight on. Clark confronted Bizarro again at Reeves Dam and uppercut him into the air sending him into the sky where John flew up and took him up to Mars.
John later returned and said to Clark that his father would have been proud and went on to say that he could have ignored all of the phantoms that escaped the Phantom Zone but choose to take responsibility. Clark shared with John his feelings about losing Lana and how one day everyone he knew would be gone as well.
John later appears again when Kara is living with Clark, storming in and grabbing her by her throat telling her to stay away from Clark. Clark breaks the two of them up and is stunned to find out the two of them know one another. Kara states that John forced her family to leave which confuses Clark as he had been told that John and his father were allies and friends. Kara then speeds away angrily and Clark and John talk some more. John explains that her father Zor-El tried to kill Jor-El, which surprises Clark more. John tells him not to trust her as he ]states she could use that against him. Clark says she is the only family he has on Earth besides Jor-El, who is just a voice. John then tells Clark to find Kara's crystal before she does or everything he knows will be destroyed.
Clark later asked John to deal with Curtis Knox, an immortal. John returned to the Kent barn after doing so and Clark asked him what he did with him. John replied by stating that him and Jor-El shared a "don't ask don't tell" policy and suggested they do the same. Clark asked if he killed Knox but John replied with the fact that he is an immortal and could not be killed. John also went on to say that Clark like Knox eventually outlive everyone he loves. Kara then returned again furious that John was still around. John said that her father was a traitor and Kara fired back saying that he was the one who couldn't be trusted. With that Clark was clearly torn between his cousin and the Martian. Kara then flew away mad that Clark took John's word over hers.
When Clark was dying after being shot by one of Oliver Queen's arrows, John appears and flies him to the Sun so he could regain his powers. Clark later wakes up in his loft with John standing over him. John throws him a football and Clark catches it and crushes it in his hands. John then tells Clark that this is the last time he will receive his help since the Sun stripped him of his abilities. Clark stated he wouldn't receive Jor-El's help either since the fortress disappeared. Clark said when he was dying he saw Lana and his parents in his dream and reflected on all the times someone had gone out of his life. Clark said he has either had someone die or walk away from him. John stated that his father was putting him on an impossible journey to have the power of a god and yet live amongst humans. Clark said he had been holding on to a life that hasn't existed for a long time. John then asked what he should do next and Clark replied with to let the past go seeing that it is the only way he can start a new one. With that John hands Clark his red jacket and puts on it ready to move forward.
Clark later met the Martian again, who introduces himself as John Jones at the scene of a recent attack on the Ace of Clubs. John tells Clark that he took a position with the Metropolis homicide division as a detective so he could be closer to Clark and help him, even without his powers. Clark felt guilty about John not having powers and stated that he will find a find to get them back. He also felt guilty that he wasn't there to stop the recent disaster but Jones tells him he can't save everyone. Jones and Clark talk about the attacks going on and both admit they don't have any leads. Clark later found a lead and gave Jones a list of meteor freaks from Chloe Sullivan's Isis Foundation group and admitted he memorized the list because him and Chloe don't agree on the case. Jones asked if Clark's coworker had an opinion. Clark reported that she was on assignment in Lubbock, covering a monster-truck rally. Jones also pointed out that Clark's "super friends" are still disbanded and Clark got annoyed. Jones noticed the food boxes littering Clark's desk and warned him about obsessing over the case. Clark said he thought Jones would be happy that he is being more proactive. Jones took the list of names but told Clark that there have been at least five similar murders in the last few months, but one paramedic had been first on the scene: Davis Bloome.
Later the presumed killer was caught and Clark became frustrated that he was so wrong about his suspicions about Davis and told Jones that even though the murderer was caught, another killer will be next. Clark said he has been working every night but will never catch them all. Jones pointed out that Clark needed to do more to make sure he does not get caught. John said he has been quelling the numerous Good Samaritan reports. Clark agreed to be more careful. Jimmy Olsen then came in and interrupted the two and noticed that Jones was a member of the force. He introduced himself and told him that he thinks the Good Samaritan saved him the night before. Jones pointedly encourages him to get hard evidence of the Good Samaritan which made Clark worried. John then left and bided the two of them good night.
After Clark and Kara managed to escape the Phantom Zone, Clark told Kara to ask the Martian Manhunter for his Martian crystal in order to capture a Phantom Zone escapee, Faora who had inhabited Lois Lane and was using her as a vessel.
John had been shot and Clark was clearly concerned for him as he watched him be pulled into the hospital. Dr. Emil Hamilton had been called to treat John's injuries and Clark was even more concerned then fearing that John could be discovered to alien. Oliver then arrived, revealing that he knows that John is Martian and that Emil is on his payroll, and that John had saved him from some police problems. Clark askd if he knew what John was working on and Oliver said no and suggested they split up and find out. Clark was determined to find out who shot Jones so he enlisted Chloe's help. Their conclusion was that Jones was shot by an officer of the Metropolis police force. Chloe managed to get Clark undercover as "Joe Fordman" a cop transferring from Coast City. Clark discovered a group of cops : Dan Turpin, Joe Simmons, and Talbert were killing conflicts and that Jones was on to them and was shot to cover it up. Clark concluded that either Simmons or Talbert could have shot John since both cops have had sniper training and Jones was shot with a sniper round. Clark was then set up by the corrupt cops and arrested for the attempted murder of John Jones. The cops then hatched a plan to kill Green Arrow but Clark escaped police custody and stopped them while Turpin had a change of heart and arrested the corrupt cops. The next morning, Clark and Oliver visited John in the Hospital who had fully recovered. Clark asked John why he didn't contact him sooner. Jones replied that it was his pride that got in the way. John then mentioned it was the same thing that keeps Ollie and Clark from asking for help. Jones mentioned that when you have so much power you get used to not asking for help. Clark talked about how he saw the brotherhood policemen have, how good it is to have someone who has your back and that sometimes you can't do it alone, no matter how powerful you are.
Season NineJohn returned to help Clark, Oliver, Chloe and the JSA. He was teamed up with Doctor Fate who used his powers to return John's powers before he was killed. Emil Hamilton found Jones and called Clark. Emil told Clark that John was going through some kind of incubation and was not sure of the end result. Clark, Oliver and the JSA fought Icicle at Watchtower and then John appeared with his powers intact, helping to defeat Icicle.
Clark asked John to fill in for him as the Blur, while he went on vacation with Lois.
When Oliver disappeared, Clark and Chloe investigated Ollie's last appearance and found John at the location. Clark super sped over to him and questioned why he was there. John hadn't heard of Oliver's disappearance and said that he was there on police business. He told Clark to trust him but Clark x-rayed him and saw an ear-piece in his pocket. Clark questioned John again but Jones flew off, leaving Clark behind. After Checkmate found out the identities of Green Arrow, The Blur and Watchtower, John used his powers to wipe Amanda Waller's memory. Later at Clark's loft, John assured Clark that his identity was safe. Clark said to John part of him wanted to agree with what Waller said that preparing for the oncoming war isn't such a bad idea. Clark conceded that eventually he will have to choose sides, but John tried to convince him that he'll be a neutral ambassador that will bring everyone together.
John was united with members of Justice League and the JSA to discuss the battle against Zod and the Kandorians. John agreed with Chloe that they should stay with Clark's plan and wait for him. Clark announced his plan to leave with the Kandorians forever using the Book of Rao and that they should protect the world in his absence. John nodded his head in agreement and then signed out.
Clark, John, and the rest of the league were all present at Carter Hall's funeral. A mysterious white pyramid object then rose out of Carter's tomb and flashed a blinding light which rendered them all unconscious.
- John Jones helped Clark defeat three Zoners: Aldar, Dr. Hudson and Bizarro.
- John has teamed up with two of Clark's parents to protect him. He agreed to look after Clark for the sake of his biological father Jor-El, and then again later worked with Martha Kent (as the Red Queen) to protect Clark from Checkmate.