When she gets back to Smallville, she makes a run by the Torch; Pete's there and he informs her that Lionel took  away all the donated computers to the school as well in edition to firingher and her father in the last episode.   She's upset and starts walking out to her car when a red pick-up truck chases her across the parking lot; she dives to the ground moments before it smashes into a van.   She gets up and looks at the driver: a very confused Clark Kent.  They both go to the hospital where Clark's given a breathalyzer and he says he doesn't remember what happened at all; the last thing he remembers is working on his history paper.   Chloe shares a look with him before adding that it looked like he "lost control of the truck" and having him shooed out of the room.

The next morning, she confronts Clark in his barn where she tells him she wants to know the real reason he tried to run her over; Clark's confused until she spells out that she was "covering for [him]."  She says that she's not sure if he'd do it or not, he rebuts that she's "not who [she] used to be."  Chloe points out his Metropolis summer ("kind of like running off to Metropolis and becoming a whole different person" - with Williams in the background) before going about looking for more clues to what really happened.  On his laptop she finds an un-openable letter from 'Brainwave.'

Later that day, Lana gets hit with the same email and attacks Chloe in Smallville High with an axe getting them both suspended.   They regroup with Clark and Adam in the Talon where Chloe jokes "someone is officially trying to kill [her]" and she figures out that Brainwave has struck twice.  Adam helps them piece together that it must be some massively power hypnotic suggestion, and that the reason it wasn't sent to Chloe herself was because our survival instinct would override it. Adam traces the signal back to her HD from the old Torch machine (which is now missing from LuthorCorp). 

Chloe goes into the Torch at night the day after; Clark's there doing research and startles her.  He's found the images of the woman who stole Chloe's computer from LuthorCorp.  Chloe recognizes her as Molly Griggs, a former teen genius who had a mental break down and was sent to Summerholt Neurological Institute.   She says that ever since what happened to Ryan, she's been looking into Dr. Garner and Molly had given her enough information to shut Garner down for good.  Clark has her call Max Taylor to warn him; Max doesn't seem to understand the danger.  Max thinks that she's on to something and warns her not to be scared off -- right before his Brainwaved secretary went homicidal.

Clark and Chloe go to visit Lex the day after; Lex comments that she really must of had Garner "over a barrel" with her article if he'd go after her like this.   She says it's a "nasty habit" that she's picked up by continually getting in over her head.  Lex is intrigued by the possibilities that Garner has opened up; Clark decides to talk to Garner telling Chloe that he'll be find and he'll call her if he finds out anything.  Lex tells her to make herself comfortable that he's going to go check on his men who are tracking Molly.

That night, she gets a phone call to go out to the barn where Martha and Jonathan have gone Brainwave on her; Jonathan has her chained to a post and Martha comes after her with a cycle.  Chloe kicks Martha out and Clark shows up from apprehending Molly just in time to show down with his father.   Jonathan however, has kryptonite and starts slugging Clark; Chloe drops the loft's supply of hay on all three which knocks both of the Kents out of it. 

Later, Clark and Chloe regroup at the Torch; Lex has given the school it's computers back without any strings attached.   Chloe admits that she feels she kind of deserves what happened as it was a payback for her deal with Lionel.   Clark replies that she can't take all the blame, if he hadn't pushed her around then she never would of caved in the first place.  She says she didn't set out to hurt him, that she was just so flattered and she just caved in when Lionel laid the Daily Planet in front of her.  Clark says she gave him a second choice that summer and he at least owes her that much.   He tells her there are "things that will never add up."   Chloe chastises him that she '[knows] that" and agrees to stop looking.   They agree to see each other tomorrow.*

*  The song in this scene is  Hoobastank's "The Reason" which is about restarting a relationship after discovering what is imporant.