I can see this crossover happening in a very reasonable way, though I heavily think Twilight Princess instead of Skyward Sword as the point from where it continues:



An exile of the kingdom where he was once called the Hero of Twilight and cursed by the Goddesses, Link travels to Skyrim following rumors and legends about the Dwemer and the Elder Scrolls, hoping they might hold the key to the Twilight Realm; namely, in crossing to them, so he could be with whom his heart belonged: Midna.



After resigning from his post as Captain of the Royal Guard, Link traveled back to the Arbiter's Grounds, hoping the Sages could tell him of some way to restore the Mirror of Twilight, or perhaps another way to cross to the Twilight Realm. Instead, he was attacked, shackled in chains of light by the Sages, before being confronted with the Golden Goddesses, Din, Farore, and Nayru, furious that he had rejected the advances of their mother, Hylia, bound to mortality as Zelda, confused by his utter lack of affection towards her. Believing that "this reincarnation" had been corrupted, the Goddesses intended to "purge" Link and begin the next cycle, only for Link to be saved by the Triforce of Power, inherited when Link proved himself more powerful than Ganondorf, becoming it's new master. This, though, was only taken as confirmation of Link's corruption, and the Sages would have joined the Goddesses in destroying Link, had he not been saved before they could recover from their shock, stolen away by what looked like a swarm of fireflies.



Explaining all that had happened to Navi, the Great Fairy from the Cave of Ordeals, Link helped her to understand the situation, which she returned in kind. Navi told Link that he was NOT the Hero's Soul bound in the cycle of reincarnation with Demise and the Goddess Hylia, but the Hero's Shade he had encountered along his journey. Having died and fell to a purgatory realm called Termina while a child, the Hero of Time Link was given his life back by a fallen deity named Oni, a fierce warrior who once a God of War and Guardian of Souls, guiding souls between the lands of the living and dead. Oni had rejected the advances of one of Hylia's daughters in favor of whom truly held his heart, Majora, the first of five sibling deities that aided the dead of Termina in finding peace, and for whom he had destroyed the Kingdom of Ikana because their claims to have mastered and conquered death angered her. Both were punished by the Goddesses, first Oni, then Majora when she sought them out to take revenge, he simply imprisoned, while she was imprisoned and cursed to forever relive her failure, driving her insane. Majora's divine symbol was The Moon; and Oni's The Wolf.



Through Oni's power, the Hero of Time Link returned to the Lost Woods, continued and finished his journey to find his old friend, Navi, before returning to Hyrule to protect it, and had, growing into a man as he did. But then Ganondorf had released a mistake the Goddesses had made, for they had forced him to face his opposite, his "shadow", and in doing so, created the Scourge of Time; an evil version of Link consumed by Death and wielding the Triforce of Power and a corrupted Master Sword. Despite having defeated the Scourge of Time in the past, the Hero of Time could not destroy him, not on his own, so joined his soul with Oni's, and removed the Source of Time from existence.



However, Hyrule had been ravaged by the conflict, and would continue to be so long as Oni/Link remained, their presence disrupting the balance, so Din, Farore, and Nayru exiled Link from Hyrule so his soul could be purged, using their power to separate Link and Oni's souls and, once Link had crossed out of Hyrule's lands, Oni's soul would fade away into oblivion. The Goddesses believed that, once that was done, the cycle of reincarnation could begin anew, as the Hero of Time and the Zelda of that era had already had a child, created before the Scourge had been released, and would be born never knowing their father.



But the Goddesses did not know that the Hero of Time, on his way out of Hyrule, intending to travel back into the Lost Woods, would produce another child with a close friend for whom he deeply cared; Malon, the daughter of the Lon Long Ranch's owner; one into whom Oni passed on his own energy and essence alongside that of the Hero of Time. When Link left Lon Lon Ranch the next morning, he did so alone, truly alone, leaving his trusty horse Epona with Malon for one last time, upon whom she would ride out of Hyrule a few short years later, not wanting to raise her beloved child in the harsh lands Hyrule had become.



Meanwhile, Ganondorf, whose punishment the Goddesses had left in the hand of the Sages, would be executed and exiled to the "Twilight Realm"; the dark alternate timeline from where the Scourge of Time had come.



Of course, the Hero of Twilight knew now what had happened. And, from its description, Navi can only assume that the strange dimension that the Hero's Shade had taken him during their travels was Termina; or at least some small part of it.



The truth of his ancestry, that of The Hero, a nature-loving 'peasant' woman, and a fallen divine, now known, the Hero of Twilight Link departed Hyrule with Navi's aid, helping him as she had his ancestor, knowing the Goddesses would never believe the truth or accept the fact that their actions had already broken the cycle and would lead to Hyrule's doom.



They teleported to the Temple of Time so Link could retrieve the Master Sword, needing its power against the evil and corrupt to protect him from the Goddesses' wrath if he ever wanted to see the end of his journey and reach the Twilight Realm. Hearing Link's heartfelt pleas, the Master Sword came free of its pedestal, it's inner spirit, Fi, siding with him over the Goddesses that had fallen from the righteousness and good that Fi had always served in the hands of Link and his ancestors; well, ancestor. Sadly, they were not able to act quickly enough to save Navi, whom had been fighting the Temple's guardians to give Link a chance to retrieve the Master Sword. Navi thanked Fi for helping 'my Link' once again and infused her power and energy into the Master Sword; the last aid Navi could give them as, turning on the Goddesses as she had, Fi and the Master Sword no longer drew on the Goddesses' power, but Link's own power now.



Link quickly left Hyrule after that, retrieving the equipment from his adventure which he had left in the care of Mayor Bo of Ordon, whom he advised to have people stay away from Hyrule from now on. Racing across land on Epona and over seas on ship, Link has spent months, years maybe even, trying to discover a path to the Twilight Realm so he could be with Midna, knowing in his heart that she feels for him what he does for her, while also avoiding the wrath of the Golden Goddesses and their agents. He eventually learned of the Elder Scrolls, artifacts that contain knowledge that exceeds beyond any deity or dimensional realms, and believes they will be the key that he seeks. And it is the Dwemer, the ancient dead race that are rumored to have discovered a means by which to read the Elder Scrolls without risking insanity, that has led Link to Skyrim, where the 'Dwemer Decoder' and possibly even the Elder Scrolls themselves are rumored to be.





Thinking of this story, I can see a lot of big events happening. Link using the Aetherium Forge to restore the power of the Master Sword as he searches the Dwemer ruins of Skyrim. Becoming a disciple of Hircine and gaining the power to transform into his wolf form and a werewolf version as well. Restore Azura's Star and get a special crystal or version of it to use in his magic armor (the one that drained rupees for invulnerability, but would work more like a protective barrier in the story). At some point be confronted by Zelda, probably crossing paths with her in Solitude, and possibly becoming an enemy of the Empire because of her, making his life in Skyrim harder as the majority of the Nordic population is very anti-Elf, which Link would be seen as. Of course, on the flip side, he'd get help from the Hero's Shade, his ancestor, which would be perceived as some undead Thrall. I wouldn't have Link possess vast magical powers or use Shouts though, despite having the Triforce of Power; instead, his magic usage would be either small, like lighting a campfire, or a big move of desperation, like cause an earthquake or call down a thunderstorm in one strike to take down a dragon, with Link only using a handful of Shouts (force, animal aid, detect life). Link's true power would come from Songs and Howls, channeling energy into the songs he learned, and continues to learn, from Hero's Shade, alongside others, allowing him to conjure storms, destroy undead, teleport, and even manipulate time.



Damn it, why don't I have the time for these stories I think up!?