When the nightmares begin, Vin doesn't question them too much.
He begs them to go away, leave him alone to his peace, to his thoughts. Instead he gets a warped image of family, everything he values… And never has.
(That was before he created the network of course. Then he had a family, and the nightmares lessened.)
After a while, he begins to think on them. In his quiet moments, when he's not focused on Zero or a mission or any of his friends, he thinks about them. He's not too afraid anymore, because they're just dreams, he's realized that. But he still thinks on them.
(He never got dreams like this before he came to Pinkerton. He never got dreams like this before he met Macbeth.)
He dismisses the thoughts that rise in his mind, pushes them away as a bad job. But they linger, echoing and making his skull reverberate. He feels sick. He tells himself there's no way that could happen.
(He can't help but remember that she never gives him unnecessary lines, unlike the other students. He doesn't get as bad detentions as the other students.)
The network continue mocking and foiling Macbeth and her plans, and for a wonderful moment, everything is OK. He feels genuinely well. And of course Christmas passes by with his Pinkerton family and nothing could be greater.
(He tries to ignore the fact Macbeth poured her heart out to him. He tries to ignore that he didn't get a detention afterwards, even though he caused this mess in the first place.)
Everything is good again, until the Investigator arrives. Vin fears for the network and his friends. They'll be strung up if this investigator finds out who they are. It never occurs to him that Macbeth has things to hide as well.
They find the video, 'In the Prairie with my Funny Bunny Fairy' and he has to admit - it's hilarious, especially given Macbeth's strong hatred of children.
(He cant help notice her hair is luscious and blonde in her youth. He can't help but realize bunnies are his favourite animal.)
He doesn't tell anyone but he watches it again, and it is catchy too. He falls asleep listening to it, and has a strange dream of a woman with blonde hair singing it to him as he struggles to fall asleep in his dream.
(He never sees her face. He watches from the sidelines, because he's not sure if he wants to know.)
Holidays arrive, and Vin is overjoyed to be staying with Trixie. Her aunt is a nice person - he finds that out later.
(He doesn't say the reason he was so late packing up was because Macbeth called him to her office, then sent him away merely minutes afterwards, after an awkward silence stretched between the two. He wished her a good holiday and left.)
On holiday he has more time to think about it, and wonders if it's all some massive coincidence. He wonders if there really is a link, and manages to convince himself otherwise.
(He can't help remember when Macbeth went to erase his parents, she appeared. Couldn't be erased because…)
He dismisses the thoughts and for a while he forgets them. Macbeth becomes nothing more than the villain in their stories. They have great fun exaggerating her massive mistakes and defeats, and mocking her infuriated screams.
(He can't think of her as anything but a villain. He won't think of her as anything but a villain.)
Pinkerton High comes about, and the nightmares start again. His thoughts plague him once more, and he doesn't try and stop them this time. But he has no proof. No evidence, except what he has thought and seen, and that is not enough.
(He doesn't mind that much. He'd rather not have his theory confirmed.)
So he merely pushes them to the back of his mind and focuses on studying and defeating Macbeth every now and then. He's happier this way. He doesn't need parents, not with the network.
(That's what he says but the links rattle around, forming a chain in his head which he can't get out.)
On the last day of Pinkerton, everyone cries. The foursome are staying together, that much they agree. They will be friends forever, bound by the experiences of INK and everything in between.
(He's long since got together with Zero, and he can tell Macbeth disapproves. He tells himself that she hates love anyway, and it's not for any other reason.)
Macbeth is there for his leavers speech, and she pays much closer attention to his than anyone else's.
(He refuses to make eye contact with her as he makes his leavers speech about family. He's afraid of what it might reveal - and not just about INK.)
He leaves Pinkerton with a heavy heart. But he knows he's ready for the future, and whatever it may throw at him. His memories and the links slowly fade away as he gets busy with university, work, then finally crossing the family barrier with his sweetheart Zero. His life is not what he imagined, but it is still perfect.
It's only years later, when he moves back to his hometown, near Pinkerton, that links begin to show again. Zero is ecstatic - she wants to know whose taken over INK, how Mr Soper is doing and what the new kids are like. So they go to Pinkerton, where a very old Mr Soper greets them enthusiastically, with laughter from years gone by etched onto his face.
They meet the new INK after breaking into the headquarters and finding four new pre-teens there, who listen with wide eyes to their stories of Macbeth, and they look with new reverence at the equipment left behind by Newton as a gift to the new INK. They give the kids their number, promising that if the new teacher, Gunter, becomes too overwhelming, they will come to the rescue.
It's only at the end of their visit, Mr Soper pulls Vin aside and tells him that Macbeth wants to see him. She's suffering from some disease and hasn't got long left.
(Vin hears the chain growing, link by link, yard by yard.)
He goes to see her, because he is not cruel and can't deny a dying woman her last wish. But she has long since passed her sanity, hard as it may be to believe when he thought she was insane when he was a little boy. She rants, on and on, about INK, about her career as a singer, about her schemes to take over Pinkerton. Vin is nervous, but the doctors tell him she's just babbling. After all, they laugh, whose ever heard of a secret organization of children that constantly foil an evil genius' plans?
Vin is about to leave her when she says something quite unexpected.
"I knew a boy like you once. I never had the courage to tell him who I was to him. But he already knew. I could see it in his eyes. And he was trying to deny it." She looks at him closely. "But I suppose it's all done with now…" And she goes back to ranting.
(He can hear the final clank of the last link falling into place, sealing his thoughts forever, confirming what he had wondered.)
He tells Zero about Macbeth and her rants, and nothing more. She leaves school with him, still blissfully unaware of him. But it's OK. She doesn't need to know. She won't know.
He receives a letter a few years later, informing him of Macbeth's death. He can't help but miss her. She was the source of INK after all. Without her evil plans there would be no INK. No him and Zero. He owes everything to her.
(He never tells anyone, but instead vents his feelings on paper, in a letter that no one will ever see.)
He's never going to think of it again. There's no reason too. He lives quietly and happily with Zero, the thoughts fading from his mind once again.
It's only on his deathbed does he look upwards to the sky, finally accepting it as it really is for him. He utters in his final moments,
"I'm coming mum."
And the secret dies with him.
So obviously, this isn't canon... probably not even completely correct. But I had to get it out of the way, because it was banging around in my head. Probably won't write a follow up. But if you want to use the idea, go crazy! But do tell me, because I will want to read your story.