Are we seeing a Lana and Trask pairing here? Alongside another pairing, Smallville and kryptonite?
Consider the following scenario. Pete accidentally uncovers the kryptonite in Smallville. He is killed because the kryptonite has weakened Clark so severely that Clark can't help him. Lana has seen it all, and she hates Clark and blames him for Pete's death. She knows that the kryptonite can weaken Clark and maybe kill him, and she knows where to find the kryptonite.
And Jason Trask is there in this story, too:
He leaned back in his chair and gazed at the ceiling in thought. “Superman, eh? You know, it's ironic, but there was a scientist who went rogue from a government project around the time your dad and I got out of the trenches. He had always claimed that there was an alien presence on earth. He never had any proof outside of some benign bacterium from a few meteorites though.”
Lois's eyes grew wide. “What do you mean he went rogue?”
“The powers that be shut down his project and he started working on his own. He caused enough damage that they had to eventually find him and put him out of business. From what I heard, he had an extensive setup somewhere. Anything you think of that is banned or unethical was done there.”
The hairs on the back of Lois's neck stood to attention. Her gut was churning at the information – and she never ignored instinct. “What was this scientist's name?”
“Trask. Jason Trask.”
Trask suspected that there was an alien presence on the earth. What if Lana contacted him somehow, informed him about Clark, whom she knew to be an extraterrestrial, and showed him the kryptonite which could hurt or kill 'the alien'?
The problem here is that Lana cloned Clark, and I don't see Trask wanting to do that. Trask would just want to kill Clark, I think. But maybe he would like to find out more about Clark's DNA before he destroyed him?
The search for Jason Trask was not going nearly as well as she had planned.
In fact, it was a dead end, she discovered, as the link she'd clicked revealed an article from a newspaper. Jason Trask was dead.
...
Lois was convinced that Trask had been behind the collection of meteor rocks that had been commissioned around the nation all those years ago. That meant that someone, somewhere, had an immense supply of the very poison that could kill Superman.
...
Trask's operation had been shut down by the feds, but the location of his lab had never been disclosed. The fact that he was dead didn't mean that the work stopped.
No, the work that Trask had initiated hadn't stopped. And we can all guess who is keeping it going: Lana. Maybe in collaboration with someone. Luthor perhaps?
The problem for me is to understand how Lana managed to clone Clark at all. Cloning is hard, as Dr. Klein explained to Lois. As you pointed out, Sonia, it took the people behind Dolly the sheep 277 eggs to produce only one surviving cloned sheep. Of course, Lana had access to a lot of tissue from Clark - she gouged him so severely that she almost killed him - and who knows how many human eggs she might have access to? Where did she get those eggs from, though?
Another thing about cloning is that a human clone has to develop within a human womb, just like an ordinary child. As far as I can understand, a normal egg from a normal woman would have its normal "contents" removed from it, and the DNA required to make a cloned human would be inserted into the emptied egg instead. Then the egg would inserted into a womb, where it would grow into a child. In other words, a human woman had to carry Jory to term. Who was that woman? Surely not Lana herself?
I guess that if Lana had a sufficient number of eggs and women at her disposal she could try to clone Clark until she finally succeeded. But why Trask would want to spend so much time and effort to clone Clark is hard for me to understand. There is something about the connection between Trask and Lana that I don't understand.
Apart from the Trask and Lana business, this chapter contained some absolutely adorable interaction between Lois and Jory again. I absolutely loved this:
Lois slid into the den at her parent's house after letting herself inside the front door. “Did I make it?” she asked, glancing up at the clock.
“I'd say,” her mother answered, laughing while Jory jumped up from where he and Ellen were coloring in picture books on the floor.
Lois wobbled as the little boy tackled her legs.
“He didn't take a nap,” Ellen reported, standing and dropping her red crayon near the box. “He wanted to be where he could see the clock.”
The little boy was so happy to see her that he tackled her legs in his need to get close to her!
And he didn't want to take a nap because he had to be able to watch the clock the whole time, so that he knew when Lois would come back. It's just lovely.
This too is great, the warm relaxed interaction between Lois and Ellen:
“What do you guys have planned for the rest of the day?”
Lois made a face at Jory and he scrunched his nose in response. “I don't know.”
The little boy sighed and leaned forward, placing his head on Lois's shoulder and rubbing his eyes.
“Well, you should just stay for dinner. Now that you're here, the little guy can be coaxed into a nap, and you and I can catch up.”
Lois rubbed Jory's back and shrugged. “I think we can handle that.”
And this, too:
You understood everything he said?” she asked in surprise.
“Most of it,” Lois answered. “I'm getting better.”
“I didn't even know that you knew sign language,” Ellen commented as she bent to clean up the results of the coloring session.
“I didn't,” Lois answered, leaning down to rub noses with the yawning child nestled in her arms. “But then I didn't have a reason to before. Isn't that right, buddy?”
Ellen didn't look up, but a knowing smirk flashed across her face.
I love it!
The contrast between this absolutely lovely interaction between Lois, Jory and Ellen and the horrible evil lurking out there somewhere is... disturbing, to say the least.
Ann
Give him some time and he'll find a cure (of course, Lois will have to convince that lunkhead that he can trust Dr. Klein to study his biology and treat Jory - but I'm sure she'll keep 'working on it'). 
He must be extra careful with her. 
