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It was impossible to truly, completely, utterly destroy the Infinity Stones without destroying what they represent in the universe. Destroying crystallized Time, Space, Reality, Soul, Power, or Mind would destroy the concept in the universe it was from.
It was, however, possible to scatter that concept and allow it to go where it may. While it would be technically possible to reform the Stones, it would take a gathering of both the concept and the dust the original Stone had become followed by an explosion on the level of the Big Bang to provide enough energy to recondense even one, recreating the conditions under which they had originally formed. It would be practically impossible.
Stark had understood this, in his last moments. He wasn’t lauded as a genius for nothing, after all.
Strange did not understand. He was thus unprepared for what came after.
The Stones’ physical forms were destroyed by Stark, and scattered. It could be likened to dust being scattered across the universe. Space faded into everything, as it represented everything, along with Reality. Mind settled in all sentients, along with Soul. Power roamed, and accumulated where weapons of great strength were.
Time, however, was different. Because of its nature, it stayed together like it once was. As it once was contained in the Eye of Agamotto, so it was/is/would be gathered where the eye was. As it was/is/would be wielded by Dr. Strange, so it was/is/would be throughout his entire life.
It had always been odd how quickly he took to magic, after all, once he was unstuck from his past as a surgeon. It was odd how perfectly he remembered things, how he was obsessed with watches, how he remembered release dates of songs so well, how he kept perfect time. He was not quite a genius, but could make almost absurd logical leaps and know they would be correct. He was arrogant, as though he knew he was/is/would be the best wherever he applied himself.
This connection was not obvious. The Ancient One never saw or realized, as she never wielded the Eye or been close with those that had. They all had a sort of timelessness about them, knew things they shouldn’t have yet, and were impatient, as though time should be matching them instead of them matching pace with the world around them.
Of course, no others were quite as affected as Strange, though he didn’t know it yet. He wielded it to such a degree that Time itself, though it could have gathered around any of its wielders, gathered around him after its crystallized form was shattered.
After this, the changes were more obvious, for all they would not be seen immediately. It began with a certain attack, on the world and those in it, from a mystic source. It was the responsibility of Doctor Strange, Sorcerer Supreme, but he was not yet up to the task. In a moment of desperation, out of habit, he Called upon Time, like he had in his most desperate moments before--
--and Time Answered him, as it had/was/always would.
The world froze around him and slowly moved backward, as it had when he’d called upon the Time Stone against the followers of Dormammu. Unlike then, however, he moved himself back in time and felt his wounds reverse and some energy return, though it was negligible compared to the sheer amount of energy it took to channel Time.
He couldn’t help but wonder, for a few moments, if he was messing with the natural order of things, spurning the Natural Law like Mordo had claimed all those years ago, what consequences it may have, and forced himself to dismiss that thought.
(He was right.)
He destroyed the being and saved the earth, and none were the wiser, save Strange himself. Wong wondered how he knew exactly what the being could do in the first battle, but ignored it as another of Strange’s intuitive leaps that he had seen many times before.
Strange was torn on whether to ignore it or pursue it for a time. He feared the memories he associated with Time, first the unending and countless deaths he had experienced, then the measures that desperation had driven him to in so many possible futures. His intuition also whispered that this path was unnatural, that there was power and horror to be found.
However, Strange had never been/is not/will never be able to conquer his curiosity or ignore his duty. He Called, and Time once more Answered, and coalesced further around and within him, drawn by his Call. He experimented more and more, learning how to wield Time without the Eye of Agamotto, for he knew on some level that he had not/could not/would not stop once he had begun.
Wong noticed, of course, but he knew the threats the Earth faced without its Greatest Defender and without the Time Stone. He warned Strange against delving too far and watched him to ensure that he slept and ate.
It was this same knowledge that drove Strange into seeking greater power within Time to protect the earth, and guilt over his part in Stark’s death (no matter how long it had been or the lives it had saved, he had still sworn the Hippocratic Oath, after all) that dragged him deeper into the depths of what he could learn.
He learned to control the Timeflow around him, first, relearning speeding and reversing an apple’s decay as he had at the beginning (for Time is redundant, tied and wrapped up in itself, the snake consuming its own tail, and tends to repeat).
He learned to control the Timeflow of himself, to control the Timeflow of biological processes like eating, sleeping, and aging, bringing his body of the past forward while keeping his mind of the present. Through this he learned how to handle creating conflicting Timeflow on the same thing, to nudge and control certain aspects of it.
He learned to remove a thing from existence, to reverse the Timeflow of/around a single object so far that it turned back to the stardust and component elements that all things stem from.
As he learned, he changed physically. It was slow, but as Time accumulated within him and the manipulation of the Timeflow came more and more easily, his eyes gained sparks of the same green glow of the Time Stone, and would eventually lose their original color. His blood was still red, but with sparks of visible Timeflow within. He stopped needing to eat or sleep, simply reversing his personal timeflow until it was as though he had just eaten, and as a consequence Strange ceased to age. The orange sparks of his magic developed the same green of Time within it as Time became more entwined with him.
(He never touched/touches/will touch the Timeflow of the scars and shaking of his hands. Though he occasionally considered it, some things are necessary reminders, and sacred.)
Wong had not lived in the New York Sanctum for a while, training some that needed it at Kamar-Taj, but he supported Strange as well as he could. Strange stopped experimenting, as he knew what he needed to of Time, and continued his work as Sorcerer Supreme. He stopped manipulating his own Timeflow frivolously, and lived as normally as he could, for he knew the changes it had wrought in him and refused to go too far and become something both less and more than human.
Eventually, another threat came. One all earth’s heroes were called to fight, him included. The Cloak is a reassuring weight on his shoulders as he cannot help but feel like he is being watched and blamed. He feels that he should have stopped this threat earlier, that Stark would’ve noticed, that he is to blame for taking earth’s Greatest Defender away and to blame for this current threat both directly and indirectly.
He works with the remainder of the team, but attempts to avoid eye contact to prevent them from realizing what had changed within him, both to avoid their judgement and to avoid their fear that the Stones had not been destroyed.
(For a time he too had feared that Stark had failed to destroy the Stones, but the Time Stone was still gone. It had been then that he realized what Stark had, long ago; while the Stones could be destroyed, the concepts they represented would remain and some of their power could be accessed, if it was gathered and Known beforehand.)
He nearly succeeded in this avoidance, until Spider-Man nearly died, having been impaled by one of the enemy army. (Stark had wept for this child, Strange recalled, had been something of a father to him. In a few timelines, Stephen had joined him.)
And so, Strange Called, and Time Answered. The Timeflow of the battlefield was frozen and reversed by a few moments, and that particular alien was reduced to elements and stardust.
(It was, a dark part of Strange whispered, far too quick and painless for nearly killing one so precious. He whispered back that efficiency in dealing with the threat was far more important, and that fear made him forget that he had infinite time.)
(He also knew that leaning into that urge would remove some of the humanity that he would need, if he was going to remain as entwined with Time.)
Strange stopped contenting himself with fighting the hoard, and turned to focus on the enemy leader. He called a portal and bisected the alien with it while it was focused on the Scarlet Witch.
The battlefield froze for a moment, those who had not seen the execution of the leader soon realizing the shift in mood. Strange couldn’t help but raise an eyebrow at the eyes focused on him, and then recalled why he hadn’t done something similar before as the headless, enraged remnants of the enemy army charged him as one. The other Avengers tried to kill as many as they could, but the majority made it to him.
The Cloak helped by lifting him out of reach of melee weapons, but he still had to avoid the ranged weapons. He threw up a barrier, and used his Sling Ring to escape a bit farther away to buy time to set up a spell to damage the lot of them.
Eventually he dealt with the remnants of the army that way, damaging them before portalling away to do it again as the Avengers thinned the herd.
After the battle, he offered his services to help with clean-up, and reduced a few bodies to dust. No Avengers had been seriously hurt, thankfully.
He absently undid the few wounds he had sustained, and turned to see Spider-Man’s eyes on him. Strange watched as he came over, still awkwardly uncertain despite the years that had passed.
(Strange refused to dwell on the pain that uncertainty caused him. He had known Peter, had mentored him as they ran from Thanos with Tony. Peter did not know Stephen, and Stephen had caused Tony’s death. He would not blame Peter if he hated him, for all that Stephen knew Peter would be too kind to blame him.)
(That just made it hurt all the more.)
Still, Peter (Spider-Man, Stephen reminded himself, he hadn’t revealed his identity in this timeline, and Strange had no right to know it) had grown, and Strange could see the evidence of time gone by on him. He was taller, more confident, and better at small talk, it seemed.
He also had not missed Strange healing himself or saving him, and while he came over to thank him, Strange could see the considering look in his eye. He didn’t raise any concerns immediately, but Strange knew Peter Parker; he probably knew him better than he knew himself. Eventually, he thought as he portalled back to the Sanctum, the truth would come out.
There were two options before him.
The first was to do nothing. The knowledge that, perhaps, the Infinity Stones weren’t completely gone would eventually ripple outward. Though it would be impossible to recreate Thanos’s massacre, the power the Stones offer would be too much to resist.
The second was to remove that knowledge from the world. He wouldn’t kill the boy, but it would be simple to remove the knowledge from his mind, and the minds of anyone he had told. Perhaps he could even try to reverse time, undo a whole day. He would never know his limits with Time until he tested them, after all.
As he had/would always do, Strange weighed lives against each other, and made his choice.
(As he would do forevermore.)