"Our whole life you were the one person I could tell anything to, and I always did, all my secrets. But you? Everything you ever told me was a lie!.. Clark, you don't get it do you? I don't care if you're from the moon. You never trusted me. What kind of friendship is that?" - Pete Ross, Duplicity
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Pete discovers Clark secret.

Pete helped Clark find Jonathan Kent after a tornado hit Smallville. During the search, Chloe confided in Pete about her stalling relationship with Clark. Pete was sympathetic, while hiding his deeper feelings.

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Pete finds the ship.

Pete joined the football team again. When Pete stopped at the scene of an accident, he discovered Clark's spaceship. Against his parents' wishes, Clark felt that he had no choice, but to tell Pete the truth about his origins. Pete was furious at Clark for not telling him sooner. He was soon abducted by Dr. Hamilton and tortured, but he proved himself courageous and fiercely loyal by not revealing Clark Kent's secret. This made Pete realize how dangerous the secret was and why Clark kept it from him as long as he could.
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Pete is forced to use kryptonite on Clark in order to free him from Red K.

Pete proved a valuable ally to the Kent Family when Clark was accidentally exposed to Red kryptonite for the first time. No one understood Clark's erratic behavior, but Pete figured out that the red kryptonite ring was to blame. Pete helped Jonathan overpower Clark and destroy the ring, returning Clark to normal. Having learnt about Clark's origins, Pete became more involved with helping Clark defeat criminals and meteor freaks. Pete was injured when Byron Moore attacked him, but Clark ultimately defeated him. Pete also helped Clark defeat Chrissy Parker when she started absorbing people's youth by kissing them.

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Pete and Chloe infected by a parasite.

Ryan James, who was telepathic, revealed that Pete was struggling to keep Clark's secret. Nevertheless, Pete helped Clark out of trouble in return for all the times Clark had saved him. He switched Clark's DNA sample with his own to ensure that Clark's Kryptonian origins weren't discovered. He helped Clark move the ship when the feds quarantined the farm and he served as a decoy when Jonathan and Clark recovered the key and transported the ship to the hospital where it restored Martha and Clark's health. Pete also helped Clark bury refined meteor rock.

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Pete helps Clark investigate a possible Kryptonian.

Pete was with Clark when he discovered the Kawatche Caves. Later in the caves, Pete was infected by an alien parasite, which compelled him to do reckless things, including screaming out in public that Clark was an alien. Fortunately, due to Pete's unusual behavior, nobody believed Pete. When Clark tried to convince Pete to go to the hospital, he used green kryptonite to stop him. He then used red kryptonite to make Clark join in on the fun. Clark eventually saved him and Pete expressed regret for manipulating Clark the way that he did.

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Pete angrily confronts Lionel about taking his family's business.

Despite his dislike of the Luthors, when Lex introduced Lucas Luthor to him, he invited Lucas to join in his basketball match with Clark. When Clark began to get too competitive, Pete was protective of Clark and reminded him not to use his powers in front of a Luthor. Pete finally angrily confronted Lionel about taking his family's business to provide a diversion for Clark to super speed into the caves and snatched Lionel's kryptonite key.