Initially, Clark and Jor-El's relationship was turbulent, but changed and progressed over the years. Jor-El's apparent desire for Clark to conquer Earth put Clark at odds with his father, and Jor-El's questionable actions to force his son to fulfill his Kryptonian destiny further strained their relationship. However, as time went on and Jor-El's motives have been revealed to be fundamentally benevolent, Clark began to trust Jor-El, sometimes asking him for aid in overcoming problems and facing particularly challenging foes.
Despite this growing bond, Clark's continued refusal to accept his destiny has driven Jor-El to punish him on occasion, such as removing his powers or imprisoning him for a month. Despite these punishments, it is clear that Jor-El cares for his son regardless. Although they are are related by blood and they have gotten closer over the years, Clark still classes his earth father Jonathan Kent as his true father.
Jor-El sent Kal-El to Earth to save him from Krypton's destruction. Recalling the kindness that had been shown to him by Hiram and Jessica Kent during his own visit to Earth twenty-five years earlier, Jor-El decided to send Clark to Hiram and Jessica's son Jonathan Kent and his wife Martha Kent. Jor-El and Lara both placed Clark in his spaceship, simultaneously broadcasting a message to Earth, asking the people of the planet to care for their son.
Before Krypton's destruction, having discussed what would happen with her son, Lara traveled to Earth using one of the last remaining teleportation portals on Krypton and visited the Kent Farm; she was keen to discover where her son would be brought up. Despite her obvious love for her son, Lara did not seem to mind the fact that strangers would raise Kal-El and was merely happy that her son would survive the destruction of Krypton, but nevertheless seemed pleased with Jor-El's trust in the Kents.
Clark was just starting his freshman year at Smallville High School when Jonathan told him that his biological parents were from another planet; he was shocked and wondered why his biological parents sent him away.
Clark later confided in Lana Lang about his feelings for his parents, claiming to never think about them, as they were "a million light years" from this point in his life. However, when Lana pressed him, he admitted that he would want to ask them what happened in order to make sense of all the strangeness in his life.
"This is Kal-El of Krypton, our infant son, our last hope. Please protect him and deliver him from evil. We will be with you, Kal-El, all the days of your life."
Dr. Swann was also able to explain to Clark that Krypton was destroyed and, based on the way things are going on Earth, speculated that Kryptonians destroyed themselves. Clark soon received another message from Jor-El through his spaceship, which raised more questions than answers:
"On this third planet from this star Sol, you will be a god among men. They are a flawed race. Rule them with strength, my son. That is where your greatness lies."
Clark interpreted this as meaning that Jor-El sent him to conquer Earth; this made him extremely nervous, and he was keen to cut all ties to his Kryptonian heritage.
The First Test
Just a few months later, on his 16th birthday, Clark received another cryptic message from Jor-El telling him to leave Smallville to begin his journey toward his destiny. Jor-El burned a mark on Clark's chest, which he referred to as the "mark of his ancestors"; it would prove to be an instrument of control.
Not wanting to abandon the life that he had built, Clark refused to go and destroyed the ship through which Jor-El was communicating, but the blast from the exploding ship caused Martha to have a miscarriage. The guilt from this caused Clark to leave Smallville; therefore, his attempt to cut connections with his Kryptonian family backfired, as he actually damaged his relationship with his adoptive family and Jor-El was still heard, insisting that Clark will obey him eventually.
While away from Smallville, Clark wore a red kryptonite ring to further distance himself from what he used to be. Aware of Clark's disobedience and reckless behavior, Jor-El periodically caused the mark on Clark's chest to burn painfully until Clark removed the ring. Nevertheless, Clark was insistent on removing Jor-El from his life and put the ring back on as soon as the burning stopped.
Desperate to make his son accept his destiny, Jor-El made a deal with Jonathan: Jor-El agreed to give Jonathan superhuman powers to enable him to bring Clark back to Smallville; however, Jor-El insisted that Jonathan hand Clark over to him when the time came for him to fulfill his destiny. Jonathan chose to disobey Jor-El, and helped Clark stay away from him.
"Up until now, all Jor-El has been to me is some distant, powerful threat." - Clark, to Jonathan, Relic
Clark later found a memory pendant that acted as a journal during Jor-El's brief visit to Earth. He was able to interface with this pendant and share his biological father's memories, and learned that Jor-El, in his youth, was also rebellious and fell in love with a human woman, Louise McCallum. Clark also learned that Jor-El met his adoptive grandfather Hiram Kent and probably chose Jonathan and Martha to become Kal-El's adoptive parents. This experience helped Clark to understand Jor-El better, and he began to feel that he and Jor-El were not as different as he imagined.
One year later, a near-fatal treatment to restore lost memories allowed Clark to relive his earliest memory of his Kryptonian parents placing him inside the ship, granting him his first look at his mother Lara and providing him with some hope that his parents hadn't been the monsters he'd assumed they'd been in the past. Clark began to understand that Jor-El cared for him, a fact that was further reinforced when Jor-El apparently temporarily granted Jonathan the power to heal Clark after he was wounded by the Starblade.
"Go with Kara, Kal-El." - Jor-El, to Clark, Covenant
Jor-El eventually decided to collect the debt that he was owed from his deal with Jonathan, so sent a brainwashed girl named "Kara" who thought she was also from Krypton to get Clark to return to him through a passage in the wall inside the Kawatche Caves. Having now discovered more about Jor-El, Clark was slightly more trusting towards him, although he was still reluctant to give up his life in Smallville until "Kara" mentioned Lara. Clark's desire to get to know his birth mother helped to convince him to submit himself to Jor-El.
However, Chloe Sullivan discovered that "Kara" was really a local girl that had been missing since the meteor shower; this revelation came too late, as Clark was already at the Kawatche Caves. As Clark had second thoughts, Jor-El threatened to kill Jonathan. The lengths that Jor-El was prepared to go to indicated how much he valued Clark and wanted him to fulfill his destiny. Clearly valuing the life of his adoptive father over his biological father, Clark gave in to spare Jonathan's life. As a result, Clark spent the subsequent three months being reprogrammed by Jor-El to become his Kryptonian counterpart Kal-El.
The Stones of Power
"I sent you here to unite the three elements, yet you chose to deny your heritage. Today, you shall witness the consequences." – Jor-El, to Clark, Commencement
Reborn as Kal-El of Krypton, Clark was far more obedient to Jor-El's requests. He set out on a crusade to recover the Stones of Power. However, after Kal-El recovered the Crystal of Fire, Martha managed to break Jor-El's hold over Clark by using black kryptonite to separate Clark from Kal-El, who was subsequently eliminated by Clark using the black kryptonite. Clark subsequently lost contact with Jor-El for a while.
Just before Dr. Swann died, he sent a message to Clark encouraging him to reconnect with Jor-El in order to complete his mission. Trusting Dr. Swann, Clark went to the Kawatche Caves to ask Jor-El what that mission was. Jor-El explained to Clark about the Stones of Power, and Clark agreed to take on the challenge to find them; this marked a noticeable change in their relationship, as Jor-El was offering help and guidance rather than forcefully controlling Clark. This helped Clark to trust Jor-El, and told Martha and Jonathan that he believed that Jor-El's previous actions were testing him to prepare him for the challenge of uniting the stones.
As Clark failed his challenge, Jor-El warned Clark of the impending threat since the Crystal of Air was stained with the blood of Genevieve Teague; he seemed angry and disappointed in his son for denying his Kryptonian heritage, which made Clark uneasy.
The Fortress of Solitude
Clark ultimately did unite the Stones of Power, which merged to become the Crystal of Knowledge and transported him to the Arctic Circle, where the Crystal of Knowledge was 'planted' and grew into the Fortress of Solitude, a vast Kryptonian repository where Jor-El's essence was stored. Jor-El welcomed Clark and was pleased with him, but insisted that Clark begin his training. However, Clark still prioritized his family and friends, and when Chloe was in need of help, he pleaded with Jor-El to let him go for the time being. Jor-El was reluctant at first, but agreed as long as Clark would return to the Fortress before sunset. When Clark failed to return, Jor-El removed Clark's powers as a punishment.
Clark was pleased to live a normal life, but when he died after a confrontation with Gabriel Duncan, Jor-El resurrected him with all of his powers. Despite Clark's defiance, Jor-El could not let his only son die, and used Lionel Luthor as his Kryptonian vessel to talk to Clark. Jor-El remained strict with Clark for his disobedience, insisting that, in return for restoring his life, one of his loved ones would die. Clark was angry about this, but Jor-El simply stated that this was Clark's fault for defying him. Despite this, before Clark returned to Smallville, Jor-El assured Clark that he would always love him, but Clark remained angry with him.
When Martha contracted a Kryptonian virus, Clark was briefly convinced that Jor-El was responsible. After confiding in a fellow Kryptonian named Milton Fine, Clark was led to believe that Jor-El was a ruthless dictator who imprisoned anyone who opposed him and caused similar injuries to political dissidents on Krypton. Fine insisted that Jor-El destroyed Krypton and sent Clark to Earth to conquer its people and re-create Krypton. Following Jor-El's previous extreme actions, Clark didn't need much convincing to believe Fine. However, when Clark approached Jor-El in the Fortress, Jor-El denied attacking Martha. Their relationship had clearly broken down by this point, as Clark refused to believe him and nearly released General Zod from the Phantom Zone as a result.
Understanding that Fine had actually been describing Jor-El's former nemesis and the threat that Zod posed in Krypton's past and to Earth's future, Clark's trust of his Kryptonian father began to be restored, and he even relied on his help when Lana died in a car accident. Wanting to help his son, Jor-El provided Clark with a crystal that allowed him to reset the day. Trying to spare Clark further pain, Jor-El warned Clark of the possible repercussions, which proved to be true when Jonathan died instead.
After the death of his adoptive father, Clark blamed Jor-El and cut connections with his Jor-El. This left Jor-El to resort to using Lionel as an oracle once again to warn Clark of the impending threat of Zod. With Clark and Lionel having a difficult relationship, Jor-El's choice of a Kryptonian vessel did not initially help Clark to accept the help of his Kryptonian father. However, realizing that Jor-El was the only one that could help him stop Zod from being released, Clark returned to the Fortress and became more willing to accept his help. Jor-El gave Clark a Kryptonian dagger to destroy Zod's vessel in order to prevent his release. However, once Clark realized that Lex Luthor had become the vessel for Zod, Clark was shocked by Jor-El's request to kill Lex. Clark confided in Chloe, who insisted that Jor-El had gone way beyond being a domineering father but reminded him that disobeying Jor-El had had grim consequences, but Clark chose to disobey his father again, choosing Lex's life over Jor-El's orders, despite his disagreements with Lex. As Chloe predicted, this had grave consequences, as Zod was released, Clark was trapped in the Phantom Zone, and the Fortress was shut down.
When Martha Kent's plane crashed in the Arctic Circle, she discovered the Fortress and entered it, where she talked to Jor-El. Jor-El explained his disappointment in Clark's decision to kill Milton Fine rather than deal with Zod's vessel. Nevertheless, he thanked Martha for taking care of his son, indicating how much he cared for Clark. This was the last time that Jor-El spoke for a long while, as using the Kryptonian dagger from the Fortress to kill Fine had damaged its structure. Clark felt lost after he discovered that the Fortress was dead, having now realized that Jor-El was trying to protect his son as well as Earth.
During Clark's time in the Phantom Zone, he met Jor-El's old assistant Raya, who managed to convince him that Jor-El was a good man and insisted that he trust his father. Raya helped Clark re-activate the Fortress before her demise, in the hope that Clark would go through with Jor-El's training. Although Clark was keen to rely on his father's help more and go through his training, he insisted on dealing with the other Phantom Zone escapees first, as he blamed himself for their escape and potential threat on humanity.
Once Clark took care of the escaped Zoners, he went to Jor-El to begin his training. However, with the arrival of Clark's Kryptonian cousin Kara, Jor-El decided to give Clark the more important task of keeping an eye on Kara, warning Clark to beware of her due to Jor-El's long-standing feud with Kara's father Zor-El. Kara admitted to this feud, but provided Clark with further information about his Kryptonian parents, much to Clark's delight. Kara revealed that Lara was so excited when she discovered her pregnancy, and had high hopes for her son; this pleased Clark, and he finally got to meet his mother when his curiosity got the better of him and he placed the blue crystal in the Fortress' console despite Jor-El's warnings, activating genetic duplicates of Lara and Zor-El.
Lara recognized her son immediately, and was thrilled to see him again. She embraced him and told him how proud she was of the man he had become. Clark was also excited to see her, but nervous as he had not expected this to happen. After discovering that Zor-El was also reborn, Clark became concerned for Lara's safety and hid her in Queen Tower, where she met Lana. Lara was pleased to be able to meet the people in her son's life. As a symbol of her pride in Clark, she gave him Jor-El's victory ring. Clark felt honored, yet both were unaware that the blue kryptonite that it contained would depower Clark.
After Zor-El kidnapped Lara, he admitted that he used Clark's emotions for his mother against him. Protective of her son, Lara offered to be with Zor-El forever if he spared Clark's life, indicating her commitment to ensure Clark fulfilled his destiny. Lara realized that the only way to defeat Zor-El was to destroy the blue crystal. Understanding that, by doing this, he would be killing his mother as well, Clark did not take this decision lightly. Despite their short time together, Lara and Clark had a strong bond. Lara assured Clark that she would always be with him and Clark broke the crystal, losing his mother forever.
After this, Jor-El decided to punish Clark for his disobedience once again so he imprisoned Clark in ice inside the Fortress for a month. He only released Clark when he learned that Bizarro had returned to Earth and was attempting to assume Clark's life. This broke the trust that Clark had developed in his father. However, Jor-El restored Kara's memories and powers to help save Clark when he was kidnapped by Lionel, which Clark was grateful for.
When Clark was later doubting that he had accomplished any good while on Earth, Jor-El showed him an alternate reality where he had never come to Earth, subsequently sending Clark to Krypton to save his infant self; these actions helped restore Clark's trust of Jor-El. However, following Lex's discovery of the Fortress, the Orb caused the Fortress to remove Clark's powers and make the Fortress itself to revert back into the Crystal of Knowledge.
Although Clark eventually regained his abilities thanks to the sacrifice of the Martian Manhunter, the Fortress remained inactive, as Clark was unsure if he could trust Jor-El. But when Brainiac began taking over Chloe's mind, Clark had no choice but to trust him.
During their 'reunion,' Clark confronted Jor-El about removing his powers. Understanding that Jor-El had to create a failsafe to stop his only son if he became a threat to the Earth, Clark reassured Jor-El that he was now dedicated to helping others; this made Jor-El realize that Clark had matured. Clark also said that their relationship would have to change so that Jor-El trusted Clark more than he had in the past. Coming to a mutual understanding, Jor-El helped cure Chloe; in return, Clark thanked Jor-El and called him "Father" for the first time.
Jor-El subsequently warned of the threat of a monster from Krypton that would bring destruction to Earth, and may be too powerful for even Clark to defeat. Clark agreed to take on the challenge, which pleased Jor-El and he reminded his son that he would always be there to help him. However, that proved to not be the case, as Brainiac infected the Fortress, to Clark's horror. Without the guidance of his Kryptonian father, Clark was forced to make his own decisions at the most difficult time in his life.
Embracing destiny and resuming training
After renouncing his humanity, Clark returned to The Fortress Of Solitude. Fully determined to become the hero he's destined to become and believing his humanity was his great weakness, he fully embraced his Kryptonian destiny. Once the connection to Jor-El was restored, Clark began three weeks of rigorous Kryptonian training with Jor-EL, who was pleased with his son's performance. Clark was focused and determined for three weeks until Lois Lane returned after her disappearance during Doomsday's attack. Jor-El could tell that his son was distracted by thoughts of Lois and questioned if Kal-El is truly ready to fulfill his destiny. Clark assured his father that he had left his past behind him and was keen to fulfill his destiny completely by mastering the ability to fly like his cousin Kara.
Jor-El explained that as long as he still saw himself as human he would be unable to fly, which was proved to be true during a mental trial where Clark tried to fly off of the top of the Statue of Liberty but failed. Jor-El encouraged Clark to deal with his emotions instead of ignoring them. Clark then puts his training on hold to say goodbye to Lois, but has since begun to alternate his time between working at the Planet and training with Jor-El.
Although Clark did not have the opportunity to spend much time with a clone of Jor-El created by an experiment to preserve the Kryptonian city of Kandor before he was killed by the followers of Major Zod, he was present as the clone died, the cloned Jor-El assuring Clark that he was proud of him.
Clark gained the power of persuasion through the use of gemstone kryptonite, and asked Zod if he killed Jor-El's clone. Zod replied with no and said Tess Mercer did so. Clark went off to kill her but was stopped by Chloe. Clark then found out Jor-El's real killer was Alia, after Zod killed her.
Revelation of unconditional love from his parents
"Whatever trials I put you through, I will never lose faith in you. We are confident you will become Earth's greatest savior. And never doubt that, just as you're a part of us, we will always be a part of you. Farewell, my son.'" - Jor-El and Lara.
Clark was teleported to the fortress, when Jor-El activated the Key in the barn. The console had seemingly repaired itself from its destruction at Zod's hand three weeks ago, allowing Jor-El to once again converse with Clark with ease. The Fortress had also returned to its natural appearance prior to its corruption by Brainiac two years before, with the sharpened black crystals all but gone. Jor-El told Clark that he was disappointed in seeing the vanity and pride that was beginning to manifest within his own heart, which would prohibit him from fulfilling his destiny.
Jor-El also told Clark that this great evil force could see the darkness in his heart and could use it to his advantage to control him into becoming the Earth's destroyer if he did not rid himself of his own flaws.
Clark saw Jor-El's reprimand as being too harsh and very judgmental, especially since he saw that he'd made a lot of progress as a hero after going through all the trials thus far.
Unbeknownst to Clark, although he was reprimanded by his father as a way to teach him a lesson in humility, Jor-El had faith in his son that he'd overcome his upcoming trials and come out victorious. To that end, he stored away the suit made by Martha Kent in a crystallized pillar for safekeeping until Clark became the hero he was destined to be.
However, when Kara Kent, Clark's biological cousin, returned to Metropolis in order to draw the darkness towards her, she said that Jor-El had sent her to fight the essence. Clark was shocked, and crestfallen when she revealed that his father had said that he was "no longer his son."
When Lois goes to the Fortress to plead with Jor-El to reconcile with his son. She reminded him how wonderful a man Clark has become, but also addressed her concern that while she knows that Clark loves her, he'd never be able to fully hear it with the ghost of Jor-El's disappointment in him looming over his head. When Jor-El remained silent, Lois was furious and said that Jor-El was not one-tenth the Kryptonian that Clark was and Clark was better off without him. Suddenly, Jor-El lifted her up off the ground and bathed her in blue energy in which they have a private discussion with her, until Clark arrived after helping Tess deal with Granny Goodness. He headed to the Fortress and was shocked to find Lois in what he perceived to be her in trouble. He warned Jor-El that if he hurts Lois, he would have failed all of Clark's expectations of him, and after a moment, he forcefully removed Lois from Jor-El's hold. Lois explained to Clark why she was there and begged Jor-El one last time to speak to Clark and pleaded with Clark for one last time to hear him out.
After a few moments of silence, the Fortress lit up and Jor-El and Lara appeared in the center of the Fortress with a message for Clark. It became clear that it was a message they'd prerecorded mere moments before Krypton's destruction and baby Kal-El's departure. They told him that they had sent him away to save him from not only Krypton's destruction but their own personal failures. Lara and Jor-El informed him that he was made up of the best of the both of them and Jor-El assured him that whatever trials he might have put him through, he was confident that Clark would become Earth's greatest champion and that they'd never lose faith in him or stop loving him.
Clark was teleported to an alternate universe using the mirror box where he had been raised by Lionel Luthor instead of the Kents. Clark went to the Fortress to try and get help from Jor-El, but found Lionel there with machines that were set up in the Fortress to silence Jor-El.
Clark had deactivated Jor-El and he then went to retrieve the console crystal from his barn. He was then confronted by Darkseid, who possessed the body of Lionel Luthor. Darkseid flung Clark across the barn and while in mid-air, upon Clark remembering Jonathan’s final words of guidance, Jor-El intervened and showed Clark images of his trials over the past 10 years proving that he has always had the power inside of him. Jor-El told him that this was his final trial and that he was ready to seize his destiny. Clark reawakened in the present, floating in the barn staring down Darkseid. He embraced his powers and his destiny and flew into Darkseid, presumably destroying him and the vessel he had chosen to inhabit. Clark then arrived at the fortress to be embraced by Jor-El’s presence. Jor-El told him that his journey had come to an end and that he was proud of him for embracing his heritage and who he is. He told his son that he was the only one that can lift the darkness from the Earth. Jor-El then returned the Superman suit to the surface and gave Clark his final words of wisdom, to not forget that even though he has Jor-El’s blood, he must remember his time in Smallville and his earth parents and friends that made him a hero.
In the Comics
In the Superman mythology, Kal-El's relationship with Jor-El and Lara is that of a loving family. Through the sunstone crystal in the Fortress of Solitude Superman communicates with a holographic image of his parents when he is seeking guidance . As a special tribute to his family and home planet, in the center of the Fortress Superman honored his biological parents with a statue of them holding up the planet of Krypton.
- Clark: (referring to Doomsday) I don't care how powerful it is. I'll take it on like I have everything else.
- Jor-El: I'm here for you as well, my son.
- Clark: Thank you... Father.
- Lara: My son, I only had the joy for knowing you a few weeks. I wish I could be with you always to guide you and protect you.
- Jor-El: We don’t have much time.
- Lara: My dearest Kal-El, our love will always be with you. I can already see you carry within your father's independent spirit.
- Jor-El: But, more importantly, your mother’s never-ending bravery and her compassionate heart.
- Lara: Your father tells me that the new world you're journeying to, Earth, is full of complicated beings capable of great emotion. My wish is for you to live a full and wonderful life, but I need you to know that you were born of a great love. And, your brilliant father has devised a way for you to carry on that love without us.
- Jor-El: The ship that I designed to carry you to your destiny can only hold one Kryptonian, one who has so much potential, so unlike your father.
- Lara: No.
- Jor-El: Your mother and I cannot come with you, to do so would burden your innocent soul with our frailties and failures. But you have within you the best of both of us, and I am sending you with all of my knowledge and none of my ego or regrets. They will die with me here on Krypton. Whatever trials I put you through, I will never lose faith in you.
- Lara: (Whispers to Jor-El.) Quickly, before it's too late. We may not have been able to save our planet...
- Jor-El: But we are confident you will become Earth's greatest savior. And never doubt that, just as you're a part of us, we will always be a part of you. Farewell, my son.
- Lara: Farewell.