Part 1 of my outline covering the rest of The Last Son of Krypton:

Luthor makes the trip to the fertilizer plant. As he touches base with Vale then visits Subject One in her cell, we learn more about Subject One. The same time Clark's stasis matrix arrived in Smallville, hers touched down in another part of the country, crashing and causing a devastating fire in a munitions factory owned by Luthor Incorporated. The matrix was found undamaged and Subject One retrieved soon after, whereupon she was taken into captivity and subjected to scientific observation/experimentation. While not a constant presence in her life, Luthor's the only person she knows who's shown her any affection, having given her gifts on the occasions he's visited her in the past. It's obvious, however, that Luthor's tenderness is purely performative, the ruse of a charismatic manipulator, that the gifts he's given her — mostly in the form of books authored by figures such as Hobbes and Poe — were curated to make her subservient to him and fearful of the outside world.

Through guilt-tripping and bribery, Luthor wheedles out of Subject One knowledge of her super-hearing. He then tells her of the stasis matrix, the disc found within it, and his desire to learn their secrets, persuading her to interact with them and pass on anything they reveal to him. Under controlled conditions, Subject One's taken to the laboratory housing her matrix and given the disc. Upon finding a niche the exact shape/size of the disc in the matrix's side, she inserts it. Upon doing so, she's thrown back, suffering a violent seizure which leaves her catatonic. Vale performs cerebral angiography on Subject One, but the underlying cause of her condition eludes them. Luthor orders Subject One fitted with a feeding tube and placed under observation until further tests can be arranged. Unbeknownst to her keepers, Subject One's feigning her affliction. No longer periodically exposed to red kryptonite, her powers gradually return in 72 hours. Then using her x-ray vision to map the layout of the plant, she speedily neutralizes her guards, retrieves the disc, and escapes.

Using her disc as a homing device, Subject One makes the trek from Metropolis to Smallville. Along the way, she crosses paths with a gas trucker who attempts to sexually assault her. Brutally disabling him, she tears his truck apart in a fit of rage, causing a tremendous explosion. The conflagration incinerates her clothing but leaves her unscathed.

Clark pursues his relationship with Helen in secret. Though neither his schoolwork nor chores suffer, he neglects his friendship with Lana and Pete, who've started dating. The amount of time he spends with Helen also draws Jonathan's ire, who's suspicious of Helen's intentions.

Subject One arrives in Smallville. She follows the disc to the Kent farm and begins discretely spying on the Kents. It isn't long before she learns Clark's the one she's looking for.

Early one morning, just before sunrise, Kenny pays Clark a visit. Frantic, he tells Clark that he shot and killed his father and needs Clark's help disposing of the body and gun. Clark reluctantly accompanies Kenny into the woods with the corpse. As Kenny begins digging the grave, Clark changes his mind about helping him, urging Kenny to turn himself in to the police. As the two boys argue, Subject One, who's been tailing them, reveals herself. Taken by surprise, Kenny reflexively fires at the naked girl. Uninjured but angered, she grabs Kenny's gun hand, crushing both, but Clark's able to talk her down before she can do him any worse harm.

Clark takes Subject One back to the farm, leaving her in the care of his parents while he goes back for Kenny. He finds Kenny back at his home where he prevents him from committing suicide, revealing his powers in the process. The sheriff arrives and takes a bewildered Kenny into custody.

With the Kents, Subject One's clothed and fed. Though claiming to have amnesia, she recalls that her name's Mala. Initially reserved around Martha and Jonathan, Mala warms up to them the more time she spends with them — helping Jonathan with firewood, receiving a haircut from Martha, etc. — though only truly relaxes when alone with Clark.

After Lana catches Helen and Clark in bed together, Clark confides in her that his relationship with her aunt's purely physical and unfulfilling emotionally. He stops seeing Helen shortly thereafter.

As Thanksgiving approaches, Helen invites the Kents to join her and her sister's family at her house for Thanksgiving dinner. Mala, passed off as a distant relative, accompanies them. Upon meeting Helen, Mala takes an immediate disliking to her. After Helen pressures Clark to assist her in the kitchen, the dinner commences. Immediately, Helen acts passive-aggressively toward her guests, with especial attention given to Clark and Jonathan, the gibes and innuendoes growing less passive and more aggressive as time presses on. Tensions mount until finally Helen shoves a pecan pie in Martha's face. Pandemonium ensues. Screaming at Clark that he's just like his father, she slaps him across the face, breaking her hand in the process. Mala grabs Helen by the throat, holding her aloft, choking her until the others persuade her to drop her. Falling to her knees, Helen breaks down crying.

Later that night, back at the farm, Clark and Jonathan have a private conversation in the barn. Jonathan reveals to Clark that years ago, he had an affair with Helen. Sad and angry at Martha's inability to have children, he went to bed with Helen out of spite. But when Clark entered their lives, Jonathan and Martha were able to reconnect and his love for her was restored. He immediately ended things with Helen, but never told Martha of his infidelity. Clark advises his father that the time's come to tell her. Jonathan agrees and goes inside. From the barn, Clark spies Jonathan telling Martha everything. She's heartbroken.

Mala joins Clark in the barn and they have a brief conversation on human nature; her appraisal's decidedly cynical while his is cautiously optimistic. She then confides in him, revealing that she was never amnesiac. She tells him of her life imprisoned, of the years subjected to cold, clinical experiments devised by amoral scientists, that the little love she received was false, that she was never given a name, only a number. Then she tells him she does have a name: Mala-Sonn, genetic offspring of Sela-Sonn and Dax-Ur. She tells him of Krypton, doomed to explode, and the Kryptonians, genetically bound to their planet, doomed to perish with it. She tells him that she and he were of 144,000 Kryptonian supermen genetically engineered to live free of Krypton and thrive as gods on Earth. Taking Clark's hands in hers, she levitates them off the ground, revealing that she's capable of flight. She tells Clark it's time he learned who he is and accept his destiny.

Clark and Mala visit his stasis matrix, disc in hand. He asks Mala what the "S" stands for. She tells him it's had many meanings across the millennia — it's been a Raoist religious icon, a family crest for the great houses, a symbol for hope. Over and above all, it represents Krypton itself. Inserting the disc into its niche, Clark's greeted by an AI gatekeeper, the Voice of Rao. The Voice touches Clark's brow, and in an instant Clark's bequeathed with understanding of Kryptonian languages, technology, history, and his own identity; he's Kal-El, genetic offspring of Jor-El and Lara-Van.

The stasis matrix then transmogrifies into a pedestal which transport Clark and Mala across the world to the Fortress of Solitude in Antarctica. Accessing the Fortress' computer, Mala brings up a display of Earth marking the whereabouts of all the stasis matrices across the globe. Mala tells Clark that they must seek out their brethren, then together reshape humanity according to proper Kryptonian ways. Clark tells her that for all he's discovered of his heritage, none of it defines him. Krypton may've bred and bore him, but Earth made him who he is. He'll always cherish the memories of Krypton given to him, but he won't be party to colonialism. He urges Mala to come back with him to Smallville to think things through. Mala hesitantly agrees.