Chloe begins researching Clark's background in the first season episode "Zero" as part of a school assignment. She becomes increasingly curious and soon begins digging into Clark's adoption files. Though she promised to drop her investigation after a falling-out with Clark, Chloe saves the files she retrieves, which she later passes to Lionel. In the second season episode "Lineage", Chloe reveals that she had covertly researched Clark's biological lineage, which shocks Clark and nearly ends their friendship. Clark asks Chloe to stop digging, and rather than risk further damage to their friendship, she complies.
A few months after Lionel's conviction, Chloe learns of Clark's powers from a "demonstration" staged by Alicia Baker in Season 4's "Pariah." Alicia forces Chloe into her car by teleporting both of them into it and, while driving at a reckless speed, calls Clark on her cell phone and claims that her car is out of control. Alicia then uses her power to teleport her and Chloe to a safe distance. As Alicia had planned, a shocked Chloe witnesses Clark arrive at super-speed and catch the speeding car. Clark then leaves, unaware that he has been observed.
Though unsettled, Chloe decides not to reveal Clark's secret to anyone. Instead, throughout the fourth season, she drops hints to Clark that she knows of his powers, initially believing Clark to be a meteor freak, rather than an alien. In "Spirit," Chloe witnesses the effect of Kryptonite on Clark when Jonathan Kent uses it to subdue Clark after he is possessed by the spirit of a vengeful student. Chloe pretends to be knocked out and acts as if she knew nothing at all.
When Clark is struck with amnesia in "Blank", Chloe re-mentors him on his powers and walks him through a tenuous exchange with Lex. After Clark regains his memories, he can no longer remember that Chloe knows his secret. When pressed, Chloe simply remarks that Clark had "trusted" her and seems satisfied that she was there when he finally needed her support.
In the season four finale "Commencement", Chloe graduates from high school (although her name is not called due to a military interruption announcing an impending meteor shower). She later discovers a Kryptonite-weakened Clark in Lex Luthor's walk-in safe and pulls him to safety. When Lex finds her in his office, he begins acting neurotic and forcibly drags Chloe to the Kawatche Caves. There, Chloe knocks Lex down to prevent him from seeing Clark enter a hidden chamber in the caves.
Chloe follows Clark to the Fortress of Solitude.Chloe is transported with Clark to the Arctic in the season five premiere "Arrival". She wakes up in front of the Fortress of Solitude, and is nearly killed from the extreme cold until Clark begs Jor-El to let him leave so he can save Chloe's life, and Jor-El reluctantly agrees. Clark takes her to a hospital in the Yukon, where Chloe tells Clark that she knows his secret and promises to never be the "iceberg to [his] Titanic." With no reason to hide anymore, Clark confides that he is an alien, not a meteor freak.
Since then, the pair has worked as partners to help conceal Clark's powers and face his most lethal enemies yet, namely Brainiac. At the end of Season Five, the entire Daily Planet building goes haywire when Brainiac unleashes a computer virus that infects every computer system on Earth. Chloe, afraid she will never see Clark again, kisses Clark passionately, who kisses her back. She promises to leave Metropolis, but the city erupts into mass riots. Chloe frantically bangs on the window of a passing limousine belonging to Lionel Luthor outside the Daily Planet. He lets her inside, but the rioters overrun the car. Chloe is pulled out through a smashed window by the mob while Lionel is attacked on the opposite side. Fortunately, Lionel is able to fend off the rioters with the help of his bodyguard, and they escape into LuthorCorp Plaza. The two regroup in Lionel's office, and after agreeing that something has to be done about General Zod, who has possessed Lex's body, Lionel elects to return to the Kent Farm and find the dagger Clark received from Jor-El to stop Zod. With her leg injured in the riots, Chloe returns to the Daily Planet to try and decipher the Kryptonian symbols they believe will give them clues to defeat Zod. Before wishing her good luck, Lionel gives Chloe a handgun, just in case.
While working in the Daily Planet basement, Chloe runs into an old friend: Jimmy Olsen, who was working his first day at the Daily Planet as a photographer when all hell broke loose. Chloe and Jimmy rekindle a whirlwind relationship they started when she was an intern in high school. However, Clark's reaction to the kiss they shared is unclear. Continuing to be Clark's sidekick, Chloe helps a fledgling version of the Justice League on their first mission, but she stays in Smallville with Clark when they leave.
