4.02, Gone

Clark spends most of the episode poking around for clues to what happened to Chloe, where she went; her cousin doesn't believe him at first.  Clark ends up crashing a helicopter that prevents him and her cousin from snooping around as much as he would like.  His parents find out after they catch her cousin hanging out in the bathroom with him despite his complaints, his warning that his parents won't like it, and her own promise to keep her mouth shut.

Lex and Lionel have a conversation about Chloe.  Lionel remarks that even if she "was" alive, there is no way a jury will convict him and tries to tell Lex that his own actions killed Chloe.   Lex says no that he's not buying that "bright young woman" demise was his fault at all.  Lionel Luthor then later sends a metallic shape shifting hit man named Trent to check and make sure Chloe Sullivan really isn't in Smallville, now double checking his bomb after he was tipped off inadvertently in the last episodes by Chloe's cousin in the prior episode.  Her cousin sneaks out and digs up Chloe's grave during mid-day, happy to find that Clark was right.   EDLois is then caught by Trent who now knows for certain than Chloe Sullivan is not dead,  and that he must now find Chloe and kill her.   Lois gets in a fight with him but the recently returned Lana Lang is the one who ends up chasing him off (thus saving her life) and giving her a ride to the farm.

Chloe's uncle, Lieutenant General Sam Lane, comes to the farm that night to pick "his little Lo" after Clark and Chloe's cousin realize that LuthorCorp paid for Chloe's funereal.  We also find out that her cousin was never to go near the exploded safe house.  Clark goes to Lex to talk about what happened and Lex tells Clark that the explosion didn't leave any body left to be buried.  Clark, however, recognizes the cigar on Lex's table after meet Sam Lane and walks out without talking to Lex about it.

She was one of the first undercover female reporters. She was Chloe's hero.

Clark sneaks onto Fort Ryan and into General Sam's office where he sees EDLois riffling through her father's office.  He tells her his theory that Lex is working with her father and she agrees it's possible.  She tells him that her dad is a little over protective because he lost her mom when she was six, fifteen years ago.  (Putting the character firmly at twenty-one).*  We find out that her father was doting and sent helicopters to watch over her at prom.*   While looking through the log books, EDLois is happy that her father seemingly has a girlfriend.

Clark notices the name is Nellie Blye; he knows that she died over 80 years ago.  The cousin is clueless**.  "She was one of the first undercover female reporters. She was Chloe's hero," Clark points out putting the clue together and using the address from the book to find Chloe's new safe house.   When he gets there, however, the house' security is already dead; he notices a mock Wall of Weird on the wall.   In the background, "A Long Way" by Dara Shindler is still running on her computer.  Clark notices the blood on the door and that Chloe isn't there; then Lex arrives.

Clark and Lex fight about what happened; Clark points out that Lex has a tracking bracelet on Chloe and that he couldn't think she was that safe.   He's angry that the "cost of doing the right thing" might be paid with Chloe's life.   Lex negates it saying that he saved Chloe and her father by sneaking them out through tunnels underneath her save house before it exploded (during Covenant).  Lex also says he brought Sam Lane in because he could no longer trust the FBI (understandable after the Loeder arc.)   Lex finds out that she's at the old foundry, interestingly enough, where Clark's first showdown in Metamorphosis was.

Chloe is tied, taped, and chained up in the Foundry, suspended from a hook and bleeding.   In typical fashion, she works herself over to the controls, gets down, gets the tape off her mouth but before she can untie her hands, Trent catches her and starts to choke her.  Just as it looks like he might kill her, Clark shows up and shoves Trent off of her.  Chloe falls to the floor.  Clark stalks after Trent fighting, but Trent's ability to go liquid causes Clark to fall.   EDLois shows up out of no where with a huge stun gun, and the pair end up sending Trent into molten metal.   Clark asks her how she got there, but it's never answered in the narrative.

Clark picks Chloe up off the floor, hugging her.  He says he "thought he'd lost [her]."  They share a moment before Chloe notices her cousin, whom she hugs.  EDLois tries to take the credit for finding her, and Chloe walks out saying that she'll "kick Lionel Luthor's butt in court tomorrow."  Her testimony goes well; Lionel is convicted and we see Clark reading about it in the Daily Planet as covered by Perry White.

*  The doting relationship between Lois and her father is later retconned as is her status as an only child.  There seems to be some amount of debate as to Lois' age but the canon thus far states 21 - and later sides (Recruit, Fade) that try to retcon it never make it to screen.

** This is the first example that EDLois despite having Sam Lane as a father is not all she's cracked up to be.  She doesn't have a clue who Nellie Blye is - when Nellie is Chloe's hero.  This is important, because Golden Age Lois, the original Lois, was modeled after Nellie Blye/Torchy Blane-types and Superman helped turn her into "a modern age Nellie Blye" when she recreated Nellie's trip around the world; Similarly we see Chloe recreate some of Nellie's other famouse articles over the series.  We then see Chloe work save herself (after Lois had to have Lana Lang save her from the same guy).