My basic premise of a two-hour (maybe even an extra thirty minutes) finale:
Clark is warned of betrayed loyalties from Jor-El, but at this point... Clark will have blamed everything bad in his life on Jor-El. So, what does he do? He destroys the Fortress Of Solitude, hoping to destroy Jor-El with it, seeing him as 'the ultimate source of evil'.
Back on Smallville, Lana and Lex's relationship, regardless of the outcome of this season, comes back into the fold. However, Lana becomes scared of Lex's newfound insanity due to becoming reobsessed with the possibility of him having powers much like the meteor freaks of the town. He remembers what happened to him in the cornfield as a kid, and sees it as an injustice that he didn't gain the abilities to overpower the world while everyone else in the meteor shower did. This leads to a fight between the two, and eventually, Lana is so hurt by what's happened that she leaves Smallville for good, abandoning all hope of a relationship with Clark.
Chloe, meanwhile, is stricken with a disease harvested by one of the meteor rocks during an accidental exposure. Desperate to save her, Clark goes all out to try and find the cure. He comes to Lex for help, but Lex is so taken aback by what's happened with Lana that he's gone off the deep end, and basically tries to kill Clark. Of course, Clark can't be killed by him unless he has kryptonite, so Clark's secret is... again... revealed to Lex when he defends himself.
However, unlike the other times, Lex starts to put the pieces together, and comes to the conclusion: His best friend, a man he put so much trust in, had everything he wanted. A loving mother. Good friends. Lana's love. Powers beyond those of comprehension. Lex finally tries to kill himself, but instead turns his anger onto Lionel Luthor, and kills him in a fit of rage. Devastated, He goes back to LuthorCorp, demanding his memory be erased again in the same proceedure that his dad used on him before through shock therapy.
To avoid prison time, Lex blows up the mansion, taking his father's corpse with it, and has his memory of the past few years erased. By the time he's done, Lex will have been alerted of his father's death in a blast, not knowing that he himself commited the murder. But instead of feeling morbid, He feels this as an opprotunity to seize everything, and signs the deal to fully take over LuthorCorp.
"Oh, and one other thing.", He says to his assistant. "I was considering a name change. LuthorCorp was made into a joke over the past several years... it's name tainted by my father's tyranny. LexCorp, I believe, will contradict that. Hopefully for the better."
Later on in his life, He'll blame Superman for the death of his father once seeing him use his heat-ray vision, and knowing that there's something about Superman connected to his past, though he won't know it for sure.
Clark continues trying to find the antidote for Chloe, and becomes so desperate that he comes back to the ruins of The Fortress, asking for a cure. Jor-El, who he can hear from the clouds now, refuses at first. But Clark begging for Chloe to live are moving to Jor-El, and for the first time, Clark sees a good side of his father as he provides Clark the cure.
Clark races home, but discovers that, to his horror... Chloe can't be cured by this point. She's dying. And there's nothing he can do. As they share one final embrace, with Chloe telling him how proud she is of him, and how good of a person that he is, They kiss for one final time. Though he doesn't know it at the time, her words do end up inspiring him to continue doing good for others, so she and everyone else can always be proud of him. Because that's the only reward he could ever want.
"You're meant for great things, Clark.", Chloe says, weakly. "Don't ever give up on them."
And so Chloe dies, leaving behind alot more than she could ever imagine, as Clark realises that from Jor-El's kindness in providing the cure that he's not as inhuman as once thought. After an uplifiting talk with Martha, Clark goes back to the Fortress, only to see it was rebuilt on it's own. Jor-El offers to teach Clark a new ability, in return for Clark to at least acknowledge his heritage. Clark promises to do so, and promises to honor everything taught to him from Krypton, to Smallville. Jor-El, knowing that he speaks the truth, asks Clark to place his hand on a platform in the fortress. Clark complies.
The final shots of Smallville are this:
- Clark's feet begin to levitate off of the ground, as he closes his eyes. The pedestol opens in a diamond shape, and begins to glow.
"You are meant for great things, Kal-El."
"I know. And I'm not giving up on them."
- The final shot of the series is the diamond shape projecting an image on Clark's shirt: That of the Superman emblem. The rest of the image fades, as the emblem morphs from white, to red and yellow, on a black background. Clark's journey ends. His destiny begins. Superman is born.
After that, perhaps it'd be possible for a movie detailing what happened after that, with Clark, a few years older, coming to Metropolis under advisement of Perry White after reading an article he would have done overseas on some travels.
"I did say you could come to me for a job.", Perry says. "Well, now I'm offering you something that many people couldn't even dream of, kid. You ready to take that on?"
Clark accepts the job, naturally, and begins working. Much to his surprise, however, Lois is there, working as a reporter. The two remember eachother, yes, but Clark sees Lois as a new person, given that Chloe's death obviously changed her.
"Well, someone had to keep the Sullivan legacy going.", Lois says. "Guess we had the same idea in mind."
And the rest... well, everyone knows the rest. Clark would eventually remeet Lex, though Lex wouldn't remember him. His memory wouldn't come back because of Clark's disguise. However, when Clark would eventually emerge in costume, Lex would vaguely remember his face as that of someone who betrayed him, leading to him blaming Supes for the death of Lionel.
Superman's costume would be Clark's way of 'acknowledging his heritage', aswell as inspiring hope and trust. It would be co-created by Clark and Martha, using the symbol that Clark saw in his first day of Kryptonian teachings.
Martha would live on, finding purpose in continuing what Jonathan started by keeping up the Farm, and being Clark's source of guideance, once Jor-El has taught him everything he needs to know.
Jimmy, I don't know, because I haven't seen any episodes with him in it. But he'd basically be the loser who can't get a promotion by the time Clark would come in.
Anyway, that's basically it. By the end of the stand alone movie, Clark would be Superman, Lex would be his enemy, Lois his potential love, and he will have finally felt a sense of accomplishment. If it expanded into a new series, He'd meet more familiar foes, some coming from Smallville to get a piece of 'the boyscout' from Metropolis, aswell as meeting new and old heroes, such as Aquaman, Green Arrow (Who grew a goatee), The grown Flash, and a certain caped and cowled individual from Gotham City.
