As Clark and Lana tried to make their relationship work, his powers were transferred to Lana and she began a destructive chain of events that made Clark admit to Chloe that he thought Lana had changed. Chloe decided to show him Lana’s Isis Foundation and they were shocked to realize that Lana had been spying on Lex.
When Clark’s Kryptonian uncle Zor-El tricked him into releasing a replicant of his biological mother, Clark put on a ring containing blue kryptonite that rendered him powerless. He asked Chloe to give him a ride back to his farm so he could attempt to remove the ring, and confronted and defeated Zor-El.
When Clark was frozen in the Fortress, the phantom Bizarro attempted to take over his life for several weeks. He frequently used Chloe as a resource but was less considerate than Clark, even mocking her behind her back. When he began to “forget” things, then forcefully grabbed her arm, Chloe realized that he wasn’t himself. Although Lana refused to listen, Chloe insisted that something was wrong. She stole Dax-Ur’s shield and gave it to Clark when he returned.
When Chloe admitted to secretly working for Oliver Queen, Clark was dismayed and angry at Oliver for putting her in danger. They searched for their respective cousins after Lois followed Lex to Detroit and found Kara. Clark entered a comatose Lex’s mind, but became trapped when Lex started to crash. Chloe used her powers to heal Lex and saved both him and Clark, almost killing herself in the process. Clark watched over Chloe all night for eighteen hours until she regained consciousness. He asked her not to use her power again, but she wondered aloud why she was given such an amazing gift.
When Pete Ross came to town flashing a temporary stretching power, Clark and Chloe both unsuccessfully tried to get their old friend to be discreet, but he rebuked them. They were proven right when Pete was tortured by Lex and Clark had to save him. When Clark was kidnapped and held in a cage, Lana called Chloe for help and they worked together to track down where Clark was held. Chloe was convinced that Kara was the only person that could save him, so she took Kara to the Fortress of Solitude to ask Jor-El to restore her powers. Jor-El only responded when Chloe pleaded that she loved Clark. Kara’s powers were restored and she was able to save his life.
Chloe and Clark were devastated when Lana was put into a painful catatonic state by Brainiac. She was fired from her job when Lionel Luthor left his Veritas key in her desk to give to Clark. She helped Clark track Brainiac using the resources at the Isis Foundation. Chloe helped Clark locate Edward Teague and rescued him when Teague tried to sacrifice Clark as the Traveler.
She and Clark worked together to figure out Kara’s strange behavior. Chloe decided to try to overpower Kara, but was instead attacked by Brainiac in disguise. However, her healing power weakened Brainiac enough for Clark to defeat him, and he was able to restore Chloe and Lana to full-health. When Jimmy reported that Chloe had been arrested, Clark knew that Lex was involved and fatefully went to confront him at the Fortress of Solitude.
Clark and Oliver work together to rescue Chloe from her imprisoment but in the process, Oliver fell victim of a mind-control serum and mortally wounded Clark. Against his protests, Chloe tried to heal him, but her power rendered inactive. He died in her arms, but then was saved by Martian Manhunter. Upon her return, Chloe accepted Jimmy’s marriage proposal but she waited a week before telling Clark. When Clark found out from Davis Bloome, she admitted that she wasn’t quite ready for the inevitable change in their friendship after her marriage She asked Clark if he was. Clark only said that her happiness is one of the most important things to him and that she shouldn’t worry about anything else.