If you see any mistakes with the established timeline of events, let me know. Oh, and there will be some implausible things happening, but bear with me if you can. And remember, characters are vastly different from the source material.
Lysara
A pebble falls and water ripples. In their case, so did the very fabric of what she had assumed to be true. While behavioural changes were both expected and considered when forming long term planes, changes in lordships and lives simply hadn't been expected.
The Greyjoy rebellion had begun in much the same way, with one Euron Greyjoy leading the raid on Lannisport, burning the anchored Lannister fleet and large parts of the port city. The difference, this time around, was that a small portion of the Western fleet had been conducting exercises at sea, an Ironborn oversight that would cost them much in the long term. The remaining ships in the fleet turned their vessels around and rammed into the unsuspecting raiders. Once the element of surprise was lost, however, those Lannister men were duly slaughtered by the masters of the sea. Although the number of ships the Ironborn lost was largely insignificant, Euron Greyjoy's flagship had been among those that had gone down. Enraged at having to paddle to safety, Greyjoy ordered the short-term occupation of Lannisport, and the death of any that carried the name of Lannister. Many of those who resided in the city were given shelter by loyal subjects, but there were those that were caught unaware, having presumed that the raiders would leave within hours. Some dozen blonde-haired Lannisters were killed in the space of two days, the city it took for Casterly Rock to assemble a strong enough force to repulse the traitors to the crown.
All this Lysara heard in bits and pieces for her father, the Maester and those who worked in Winterfell. Much of what she heard was nonsense, such as the rumour that the Rock itself had been stormed, and all those within were murdered and cast in molten gold.
Regardless, the situation was bad, worse than it had once may have been. In light of the fact that everything would change and so would their plans, she expected Torrhen to be just as worried and concerned at the possibility of their knowing nothing. Instead, her brother chose to get up to increasingly riskier antics, including a newfound love for climbing. When Lysara had first heard of it from her mother, of all people, the first emotion she felt was not anger, but incredulity. Had he not listened to anything she had told him? How was it possible that he was so foolish? Only then did it turn to anger. Anger at his simple refusal to make use of common sense and anger at his continued indifference to the dangers. Disregarding the obvious parallels to a raven in another world's dream, a single slip in this world would put an end to all of her ambitions and goals. She needed him, beyond all else. Out of the many thousands she would one day command, Torrhen was the only one she could count on without hesitation. But a singular moment of foolishness would leave her alone in the world. And that was a prospect that scared Lysara Stark more than she would ever reveal.
The second attack at Seagard was by all accounts a close affair, with stories and songs of Lord Mallister's bravery and prowess reaching even the North. The duel between Rodrik Greyjoy and Jason Mallister had apparently lasted for hours with neither Kraken nor Eagle giving the other the slightest edge. When her father had heard of that, he had grimly chuckled and told her that though the duel was no doubt fierce, it was also likely minutes long. In the end, as the Ironborn were being thrown back into the sea, both died at the other's blade. Greyjoy with a swift stab and Mallister hours later due to blood loss. Of course, the songs simply spoke of the two hanging off the other's blade, but the truth wasn't nearly as entertaining.
The Northern Host departed soon after under her father's command. News of Stannis' victory over the Iron Fleet off Fair Isle was met with a loud cheer when announced by her mother and a night of feasting diminished though the inhabitants of the castle may be. Although everybody spoke loudly and as often as possible that victory was all but assured for Robert and Lord Eddard, the fear of sudden death never quite went away. What if a stray arrow hit the good lord in the throat? Or an Ironborn ambush at sea? All knew that there were known in Westeros who could match the Iron Islanders on their choice of terrain, and no matter the damage dealt to the traitors, the fear ever lurked. All knew that some would die in this rebellion, as was the nature of war. Yet, each prayed that it would not be the one they cared for the most, and hoped for the mercy of the gods. Those few that worshipped the Seven remained confident in their Gods, yet those who worshipped the Old Gods worried and feared. Would the Gods of the North hold any sway in the South? At sea?
For weeks there was no word of the war, only whispers and hearsay. When word did finally come from the South, it prompted three days of celebration in Winterfell and the much-acclaimed decision by her mother to double wages for a fortnight, apparently as a tool to tie the successes of the house to that of those in service of it. Lysara thought that having family fighting for the house was loyalty enough but what did she know. She was only a child.
But while undoubtedly was joy, there hung an undercurrent of tension. After Pyke had been breached and Balon Greyjoy's head was lopped from his shoulders at the insistence of Lord Tywin, the second son of the Lord Reaper, Maron, was installed as the new Lord Greyjoy and forced to swear fealty to the Iron Thrones. To ensure further good behaviour, Lysara's father had been instructed by the King to take the youngest son to ward at Winterfell, alongside his real children.
When she heard that, Lysara had been forced to maintain a neutral expression, as she had been amongst company, but internally let out a massive sigh of relief. At least some things were going according to plan. And it was that thought that led her to wonder about the inevitability of things.
Were there pre-set routes that the game had to follow? Even if major things were changed, would the story still follow a set path? In the end, was she nothing but an ornament, to furnish and aestheticise the tale?
That she would not accept.
Torrhen
They didn't like each other from the very beginning. Theon thought that he was an up-jumped bastard too mouthy for his own good. Torrhen thought that Theon was a disrespectful shit who had not the capacity to back up his boasts. He ought to have been grovelling at Lord Stark's feet for every morsel of food, not acting as though he himself were the heir to Winterfell and not a prisoner.
The squid's obvious attraction to Lysara most certainly did not help the matter.
Unfortunately for Torrhen, Theon was both older and stronger than him. Not out of any special skill or dedication mind you, simply the benefits of age. He remembered the boy's arrival at Winterfell. A scared, lost little lamb forcibly attached to a man who had played not an insignificant role in his father's death. Greyjoy, to his credit, do not much allow that to show, choosing instead to keep his head down and take care not to particularly bother anybody around him. He sent letters, though. At least five or six ravens flew to what remained of Pyke before Theon received one back from his brother, now Lord Greyjoy. The contents of which were not revealed to any save Theon himself, who apparently had apparently sprinted from the rookery, sobbing, upon reading it. For hours, none could find him, including the whole host of guards and servants who served in Winterfell. In the end, Greyjoy had been discovered by one of the guardsmen to be hiding on the Broken Tower, refusing to come down. Lord Eddard was on the verge of having him dragged out when Lady Catelyn intervened, telling her Lord Husband she would be able to bring him out, a task all expected her to fail at. In truth, Torrhen thought that she would've come out of the tower raging, hissing her insults for all to hear. Instead, in the space of two hours, she emerged at the entrance of the structure, a red-eyed but blissfully silent Theon in hand.
Perhaps her husband's ward served as a sort of surrogate son, a healthy child with no physical defects, unlike her own spawn. This would be the son she would spoil, and nurture. This would be the boy she could take pride in, from his skill at arms to his almost female beauty.
In any case, he was soon taken under her wing, a fact that was made intimately clear to the household staff very quickly. Anything that her dear boy wanted within reason was given to him. The best of clothes, the warmest of bed-furs, and once he was old enough, the finest of mounts. While the newly-born Sansa was by no means ignored or pushed aside, the amount of attention that Lysara received had very definitively waned. The earlier years were long forgotten and obscured by the appearance of an extremely intelligent child, whose intellect was only matched by her sheer unruliness and free-minded behaviour.
And no, Torrhen was not jealous of the attention and coddling that Theon received. Not at all. That was also not the reason why he made it his relatively short-term resolution to beat the interloper in a spar. The fact that the resolution was made the day of the Broken Tower incident was nothing but coincidence.
Yes, nothing but coincidence at all.
Lysara
Torrhen's Targaryen heritage was not something that had slipped from her mind, and how could it, what with her having to look into pools of the deepest purple whenever she wanted to have a talk to him. And she did not forget to tell him, but as she would later affirm, she simply chose not to. In hindsight, it was a particularly ill-advised decision, comparable to sending thousands of men south to die in a land not of their own. But that concerned the events of another dream, a dream that would not be repeated here.
As such, she was most definitely taken aback when during a mundane conversation, her brother revealed an almost visceral hatred of the Targareyens. The conversation had shifted from a pleasantly light discourse about the history of the Seven Kingdoms to a seething rant that decried every last Targaryen monarch, from Maegor the Cruel to Daeron, the Young Dragon. He did however concede that dragons were amazing and that he wanted one. The Conciliator he had some respect for, but near none of the rest. She let him continue, an action that bought her enough time to definitively decide upon a course of action. Telling him would be the easiest way to proceed, as that would either wean him off his hatred, or draw him ever closer to her in self-loathing and disgust. Both were equally equitable choices. On the other hand, not telling him could it make easier on everybody when it came to dealing with the Targaryen princess across the Narrow Sea. And if Lord Stark ever were to tell him, a possibility seeming less and less likely by the day, she could claim ignorance and tell Torrhen that the original dream had not followed the same path. The decision should've been easy, but patently wasn't. Factoring Torrhen's near intense desire to have a family of his own simply muddied the waters further. While he'd never said, Lysara had caught him jealously regarding her own familial bonds on more than one occasion. No matter the number of times she had subtly and directly assured him that both Lord Stark and her did truly love him, and no matter the number of times he had waved her off, she knew how much he wanted the same for himself.
As usual, all that was left to her were decisions.