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- "You were always the one good thing in my life, and if I didn't tell you enough, I care about you more than you'll ever know. Please find out who did this, Clark. You're the only one who can." - Chloe Sullivan, Crusade
Chloe's cousin Lois Lane arrived in Smallville to find out the truth about her death. She and Clark began investigating Chloe's apparent murder, but discovered that she was actually alive. Lex told Clark how he saved her and her father from the blast and faked their deaths to prevent Lionel from finding them. Lionel's assassin, Trent MacGowen, found her but failed to kill her due to the combined efforts of Clark and Lois. Her testimony and voice-mail confession helped convict Lionel of the murder of his parents, landing him in prison. ("Crusade")("Gone")
When she drank a sports drink laced with a kryptonite-enhanced love potion, Chloe was transformed into an overactive devotee to Clark Kent. She joined the cheerleading squad and professed her love for him, showing up in his loft wearing only his football jersey. When her sensibilities were restored, Clark reluctantly told her that he did not have romantic feelings for her, but the two remained friends. ("Devoted")
Chloe continued her research about the strange events surrounding Smallville but also had to contend with the latent threat of Lionel Luthor. When Lionel switches bodies with Clark, he humiliated her. Lionel (in Clark's body) leaned in to kiss Chloe, but pulled back at the last second and whispered instead, "Don't you wish,", before sauntering off. Chloe nearly burst into tears and this caused another rift in her friendship with Clark. ("Transference")
On her eighteenth birthday, Chloe was possessed by a 17th Century witch, Madelyn Hibbins. With Lana and Lois (also possessed by witches), she joined a wild party and stripped Clark of his powers. When he recovered his powers, all three girls were restored to normal. ("Spell")
Around this time, Chloe began to seriously suspect that something was different about Clark. However, instead of meddling or investigating as a younger Chloe might have done, she simply stepped back and hoped Clark would come clean.
Chloe confided in Clark, revealing to him that she had found her mother in a mental hospital three months ago, being treated for a hereditary mental illness, which Chloe feared she could one day inherit. She emphasized that she felt much better having shared her secret with someone. ("Scare")
Shortly after, Chloe truly learned of Clark's powers from a "demonstration" arranged by Alicia Baker, in which she saw Clark catch a car, then super-speed away unknowingly revealing his super-strength and super-speed. She believed Clark to be a meteor freak from the meteor shower, like Alicia. Upon the advice of Lois, Chloe didn't tell Clark she knew his secret and continued to be the same good friend she always had been. However, she frequently dropped subtle hints urging Clark to tell her. ("Unsafe")
Once Chloe had discovered the secret of her best friend, she became his best ally, although he was often unaware of this. She became fiercely loyal to him and began making excuses to cover up his mysterious disappearances. Gradually, Chloe was discovering in secret the rest of Clark's powers while continued to support him in his research about the Stones of Power. ("Recruit")
Chloe was reluctantly nominated as a candidate for Prom Queen their senior year and her main competition was Dawn Stiles, the most popular girl in school. The night of the Prom, Dawn was seriously injured in a car accident, but her spirit remained behind, jumping from body to body. When Chloe won, Dawn possessed Chloe and attempted to burn down the school. When Clark tried to stop her, Dawn jumped into him and as Jonathan had to use green K to subdue her spirit and free Clark, Chloe discovered that Clark was vulnerable to the meteor rock. ("Spirit")
After Clark was struck with total amnesia, Chloe found herself teaching Clark about his own powers and learning about the ones of which she was not yet aware. She told him that she believed he was a metahuman and that she had known about his secret without him telling her, instead trusting that he would confide in her on his own time. When Clark regained his memory, he asked what he had done during the time and Chloe simply told him he did one thing differently- he trusted her. She again left it open for Clark to tell her himself. ("Blank")
Shortly before finishing the school year, Chloe was kidnapped by a meteor-infected colleague, Brendan Nash, who was obsessed with school. Nash kidnapped students from the yearbook's "most likely" list, imprisoning them in a warehouse simulated to look like Smallville High. This included Lana and other Smallville High students. Their mysterious disappearances brought Clark and Lois to search for Chloe and Lana, finally freeing them along with the other hostages still alive. That was when Chloe finally said goodbye to her years at The Torch and sadly closed the office door. ("Ageless")
Chloe's graduation ceremony was interrupted when the military announced a second meteor shower on its way to Smallville. She later discovered a kryptonite-weakened Clark in Lex Luthor's walk-in safe and pulled him to safety. When Lex found her in his office, he dragged her forcibly to the Kawatche Caves and demanded she give him answers. There, Chloe knocked him down and watched as Clark entered a chamber that mysteriously opened in the far wall. ("Commencement")