- "For the first time, I'm ready to stop running from who I really am, from my destiny." - Clark Kent, Fallout
While in the Phantom Zone, Clark found himself powerless and surrounded by deadly beings imprisoned by Jor-El. He met Raya, a Kryptonian who was one of Jor-El's assistants. Raya helped Clark escape just in time to save Martha and Lionel. Clark confronted General Zod and, after a brutal fight, used the Crystal of El to separate Zod from Lex and send him back to the Phantom Zone.
After the Dark Thursday disaster, Clark began to rebuild what Zod had destroyed, working several nights in a row. He started feeling tired and sick and sneezed so powerfully, it blew the barn door off of its hinges and almost hit Lois when she was on her morning jog. With the sneeze, Clark developed a new power: super-breath and used his newly acquired power to save Lex and Lana from a burning lab.
Clark discovered that the Green Arrow was actually Oliver Queen and revealed his powers to Oliver. Clark prevented Lois and Chloe from discovering the Green Arrow's true identity and later, with Chloe's help, Clark learned that there were more "Zoners" in other parts of the Earth and that Raya escaped the Phantom Zone as well. Clark has as objective to recapture all the fugitives and in his quest battled a female alien named Gloria and a dangerous cannibal named Aldar.When Raya found Clark and told him that he had to complete his training with Jor-El to save Earth from extinction. Together, they fought Baern, but during the battle, Baern killed Raya. After defeating Baern, Clark decided that he would begin his training after sending all of the escaped Zoners back to the Phantom Zone.
On Thanksgiving, due to Jonathan's absence and Raya's recent death, Clark told his mother that he wasn't feeling very thankful, but Martha insisted on inviting their closest friends for dinner. He also discovered that Oliver was taking a drug to speed up healing, but also caused erratic behavior and aggression. Clark unsuccessfully pleaded with Oliver to stop and ended up having to use the drug to save Lex. Oliver was suitably chastised and joined the Kents for Thanksgiving dinner, along with Lionel, Chloe, and Lois.
Clark found Javier Ramirez seeking refuge in his barn after running away from the McNally Farm. Empathizing with Javier's situation, he convinced Martha to let him locate Javier's mother and help them stay in the country.
Clark learned from Chloe that Lana may still be in love with him. Overly excited, he rushed over to the Luthor Mansion to see her, but was confronted by Lex. Denying him access, Lex told Clark that Lana was pregnant with his child. Lana came to Clark's loft to talk to him, but he told her that everything has changed. Clark also helped Oliver keep his secret from Lois and while disguised as the Green Arrow, he received his first kiss from Lois.
Clark met Bart Allen again, but when Bart was captured by Lex, he learned that Oliver had assembled a team of superhumans to stop Lex's Level 33.1 activities. Clark went to save Bart, but he was incapacitated by kryptonite. The Green Arrow rescued him and Clark joined the other heroes in their effort to blow up the facility. Oliver asked Clark to join the team, but Clark told him he was obligated to capture the Zoners first.
A Zoner, Dr. Hudson, attacked Clark and caused him to believe he was a mental patient with no superpowers. Clark was able to break free from his delusion with the help of the Martian Manhunter, the mysterious entity who had saved him from Aldar as well as Shelby whose continuous barking he was able to hear even while hallucinating.
After a recently-heartbroken Lois tried on lipstick made with red kryptonite during a Valentine's Day party, she became infatuated with Clark. Lois kissed him, causing Kal to emerge. Kal and Lois crashed Lex and Lana's engagement dinner and Kal kidnapped Lana and tried to force her to choose between him and Lex. He tried to kill Lex until Martha secretly subdued him with green kryptonite just as Lex stabbed Clark with a chisel. However, neither of them saw Lana collect the bent chisel.
Due to her engagement to Lex, Lana (and by extension, Clark) became the focus of paparazzi. Clark avoided using his powers on the farm because he always felt like he was being watched. Lana hid from a potential stalker at the Kent Farm and Clark learned that Lana had been investigating him for months. However, he still saved her.
Tobias Rice revealed that Chloe was, in fact, meteor-infected and Chloe was abducted, but returned as Clark and Jimmy Olsen frantically searched for her. Chloe made Clark X-ray her and when he located a GPS tracking device inside her, she forced him to burn it out of her. Later, Clark promised to help Chloe control her powers if she ever develops any.
When the day of Lex and Lana's wedding arrived, Clark decided to tell Lana his secret. However, unbeknownst to him, Lana had already witnessed his powers earlier that day. She promised to meet him at his barn where Clark intended to propose. However, Lionel blackmailed Lana into going through with the wedding and Clark was heartbroken as he watched Lex and Lana exchange vows.
Angered about Lana's marriage, Clark resorted to hunting down metahumans and turning them over to the police. After getting a tip from Oliver, Clark found Titan, a Zoner featured on a lethal Internet fighting ring. After persuading the emcee, Richtor Maddox, to let him into the ring, Clark had to fight Lois, who had been trying to get a story but was caught. Clark and Titan duked it out, but eventually Titan was killed by his own spike when Clark knocked him through the air.
When Chloe enlisted Clark's help to rescue her mother, who was being held captive by Lex, Clark was able to save both of them after a mind-controlled Chloe tries to shoot Lex. While Chloe was making arrangements for her mother, Moira began to slip back into her catatonic state, so Clark told her all about her daughter and her accomplishments.
After Lex was trapped in a series of underground tunnels laced with kryptonite, Lionel pleaded with Clark to rescue him. Although he located Lex, he was injured and grew weaker from the exposure to the meteorite. Lex helped him and while they tried to find a way out, they analyzed the breakdown of their friendship. Once everything had passed, Clark revealed to his mother that he felt responsible for Lex's descent into evil because he gave up on him too soon.
After Lana gets shot at the Daily Planet, Clark started to suspect that Lionel has something to do with Lana's decision to marry Lex, so he started to make his findings.
When Lois became a target for the super-soldier Wes Keenan, Clark had Lois stay with him at the Kent Farm and went to Lana to find out more about Lex's Project Ares. Clark discovered that Lex was preparing an army of super soldiers using the skills of the meteor-infected people and the Zoner he defeated weeks earlier.
The day that Clark's mother moved to Washington, Clark met Lana at the loft where she told him that she was leaving Lex and Smallville. Clark wanted her to stay and then told her the truth about himself, but Lana insisted that she needed to leave to protect him from Lionel. Clark went to Lionel´s office to confront him, but instead found the Martian Manhunter who explained that Lex was hunting the last phantom and needed to be stopped. When Clark learned that Lana had died from a car bomb while trying to leave town, he went to find Lex for revenge, but the two were confronted by the last phantom, who recognize Clark and took some of his DNA to perfect himself. The phantom took Clark's form and then threw Clark out of the Reeves Dam, destroying the place.