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- "Well, because… because I'm afraid. I mean what if I look in Mom's eyes and I see myself?" — Chloe, Tomb
Chloe and Clark were transported to the Fortress of Solitude in the Arctic and unable to withstand the sub-zero temperatures, she called out to Clark, who begged to interrupt his training to save her life. Clark took Chloe to a hospital in the Yukon and Chloe finally told Clark that she knew his secret and Clark told her that he is an alien. She became his confidante, promising to never be the "iceberg to his Titanic." Later, Lex located her and took her back to Smallville.
After Jor-El stripped Clark of his powers and Clark became mortal and when Clark's family was held hostage by deranged metahumans, the now mortal Clark turned to Chloe's resourcefulness and cleverness. Together, they retrieved a kryptonite serum from Level Three at LuthorCorp plant without his abilities.
After Gabriel Duncan, attempted to blow up Smallville with a nuclear missile and begged her to leave town so that she could survive, she and Clark confronted Gabriel, who shot and killed Clark and took Chloe to his bunker for safety. However, Jor-El brought Clark back to life and restored his powers and he stopped the missile from landing. Clark's death and resurrection was not without a price. Clark returned to his former life of keeping secrets. Chloe urged him to tell Lana the truth, but he did not take her advice.
Chloe moved into the Metropolis University dorms and scared her first roommate away with a mini version of the Wall of Weird. Lana became her new roommate after applying for late acceptance. Chloe became one step closer to her dream job of editor of the Daily Planet when she wrote a paper detailing her experiences with a vampire sorority.
Shortly after, Lionel Luthor approached her again and fed her inside information on the true identity of Milton Fine, as well as Lex's campaign for the Kansas State Senate.
Chloe went undercover along with Lois to the Windgate Club to investigate the murder of stripper Melissa Paige and then she wrote a story and obtained her first byline, which Lois and Clark applauded her for.
Chloe revealed to Martha and Jonathan Kent that she knew of Clark's abilities as she helped them to deal with Clark when he began to act differently because of being infected with Silver-K and finally reassures Clark that she would never betray him and reveal his secret.
Lois then enlisted Chloe's help in digging up information on Lex to defeat him in the election. She broke into Warehouse 15 and witnessed Professor Fine form himself from the ship. She realized that Fine was duping Clark and followed them to the Fortress of Solitude. Fine overpowered Clark with green K and opened the portal to welcome General Zod back to Earth. Chloe removed the Green K and Clark was able to defeat Fine and prevent Zod's return.
After Jonathan passed away, Martha told Chloe that she was glad she was not the only person carrying such a burden, saying that Clark was lucky to have Chloe as a friend. Chloe helped Clark work through his grief over the death of his father by helping him search for the Angel of Vengeance in Metropolis.
Chloe was seemingly driven to suicide and was treated by a psychiatrist, Dr. Sydell. She insisted that she did not try to kill herself, but no one believed her except Clark. When she began to hallucinate a vision of murdered girl, Gretchen Winters, Lana asked Lex to transfer her to Belle Reve for better care. However, Clark rescued her and took her to Lois' apartment, where the murdered girl possessed her to exact revenge on her murderer. Back to normal, Chloe had to face her anxiety over her mother's mental illness and with Clark's encouragement, went to visit her for the first time.
Chloe and Lois discovered that Clark's new girlfriend Simone had the ability to hypnotize people with an exotic amulet. At Simone's request, Clark almost killed Lex, but Chloe was able to stop him. After they broke up, Clark frequently asked Chloe about Lana's well-being until Chloe told him that she would rather not be in the middle.
However, Chloe was forced to tell Clark that Lana had become addicted to a mysterious drug. She helped him track Lana down and he was able to save her. She also gave Clark Fine's recent whereabouts, information given to her by Lionel Luthor.
Chloe was the first to discover what was happening between Lex and Lana and was shocked. Chloe and Lana had a fight when she questioned Lana's growing relationship with Lex. Both Lana and Lex responded to her questions with indignation, telling her to mind her own business.
When Clark discovered the relationship, he became angry at her too, saying she betrayed him. Chloe stood up for herself, telling Clark that Lana can date whomever she chooses and suggesting he finally get over Lana. He later apologized when he realized that she was just being a good friend for keeping Lana's confidence.
Chloe, Lois, and Martha gave Clark a surprise birthday party the same night he saw the spirit of his dead father, who instructed him to kill Lionel Luthor. Chloe found evidence that Jonathan and Lionel met on the night of his death. After the warning turned out to be a trick caused by Brainiac, Lionel revealed that he had been posing as Jor-El's oracle and had been producing pages and pages of scribbled Kryptonian characters.
Chloe used her computer skills to decipher the characters into a readable sentence. Clark was then able to read it and translated it as "Zod is coming."
Lana told Chloe about Lex being taken in by the vessel, and Chloe told Clark. When Fine downloaded a powerful virus into the electrical systems of the world, Clark went to help Chloe, but she told him that he had to leave her behind, because he couldn't save everyone.
Before he left, Chloe gave him a passionate kiss, in case they "may never see each other again." Chloe watched riots breaking out in the streets of Metropolis but escaped into Lionel Luthor's limousine. Unfortunately, the limo was attacked by an angry mob as she and Lionel were grabbed out of it.