Disclaimer: I don't own Harry Potter or Doctor Who. Also, this is CRACKFIC, you have been warned. I'd like to thank my beta, ElementalLiz, for forcing me to write this and for coming up with the title.
2000 years was a long time. Rory couldn't spend all of his time standing outside a box, and, since he knew how the world must end up for Amy to be born, meet the Doctor (and more importantly, Rory), he intervened in historical events sometimes. The Doctor might have had something to say about that, but he couldn't talk. From his research on the Doctor, Rory knew the Time Lord was a huge meddler in human history.
He didn't intervene much in major events, although he did end up very close friends with Charlemagne after the emperor took an interest in the Pandorica. Sometimes, he interfered by accident - one of the few times he got drunk, he'd ended up in a pub with two wizards and two witches and they'd had a long conversation about silly words. They'd then proceeded to make a bet over who could win in a drinking game, the two wizards on the same team or Rory. If Rory had lost, he would have had to tell them what was in the Pandorica. However, his Roman name wasn't Roranicus Awesomenus Britannicus for nothing. The wizards had lost, so they'd had to name their school after the silliest of the words - Hogwarts. Needless to say, the witches had not been pleased.
Anyway, back to Rory making sure that Amy grew up safely. He'd started to get somewhat worried, when, only a few decades before Amy was born, a new dark wizard had started getting powerful. You might say that there had been many dark wizards over the years, and you'd be right, but Rory was a badass. He didn't feel the need to get involved in stopping just any dark wizard. He had better things to do, like guarding Amy and proving that he could beat Chuck Norris in a fight (during another of those few times he'd been drunk). When Grindelwald had come to power, Rory had just gone to Hogwarts once and had a stern talking-to with their Transfiguration teacher. The next week, the magical world hadn't had to worry about Grindelwald anymore, since Dumbledore had defeated him.
However, when the self-styled Lord Voldemort tried to harness the Pandorica's power for his own in the last week of September, 1981, Rory knew he had to be stopped. Unfortunately, after said incident with Chuck Norris, his hand was a bit sore, so Voldemort only lost his body and it had taken a week for Voldemort s body to disintegrate (it might have taken a little longer, but Lily Potter's sacrifice had helped a bit). He would have rather waited the extra time, but unfortunately the Potters had already gone into hiding when he punched Voldemort. Dumbledore wasn't able to find and stop Pettigrew from telling Voldemort where the Potters were (Rory was unable to help him as he was busy that day because the Pandorica was being moved).
Rory hadn't cared about Voldemort before he'd tried to mess with the Pandorica, but since he knew that Voldemort would return, he set about making sure that Voldemort could be defeated. He'd read the Harry Potter books, so he knew that it would take many years and much arduous labor for Dumbledore and Harry to find all the horcruxes and destroy them, if he didn't help. He'd kept up his acquaintance with Dumbledore, so he knew about the prophecy, that Harry Potter would have to sacrifice himself to get rid of the horcrux in his head, and that Harry would have to cast the final curse that actually killed Voldemort. Rory was awesome and could have destroyed all the horcruxes just by thinking about it, but he needed something to occupy his time in the last few years before the Pandorica opened and Amy awoke. A bored Rory was dangerous just ask the people of Atlantis (who had tried to mess with the Pandorica around 200 AD).
He started with the ring. It was easy enough to get past Voldemort's defenses. Once he got to the horcrux, one blast from his hand-gun destroyed the bit of Voldemort's soul in the ring. He left the unmarked but destroyed horcrux in the Gaunts' house, since he knew Dumbledore would arrive to destroy the horcrux in a few years, and that Harry would need the ring to help him during the Battle of Hogwarts. It was also easy to destroy the diadem; all he had to do was ask Dumbledore to let him into the castle, go to the Room of Requirement, summon the diadem (no spell would be able to stop HIM from summoning anything he wanted), and blast it with his hand-gun. Like the ring, Voldemort's soul was destroyed, but the tiara itself was unmarked. He took the tiara; he thought that when Amy awoke she might like to see it and left a fake in its place. Although he left a note with the fake horcrux, no one ever found it, because Harry didn't see it when he moved the horcrux in his sixth year. The third horcrux he went after was the cup of Helga Hufflepuff. Anyone who said it was hard to break into Gringotts clearly hadn't met Rory Williams. He then destroyed the cup with his hand-gun, and left a note for Voldemort under a similar cup, which would eventually be covered by the multiplying goblets that were created when Harry Potter and his friends came to destroy what they thought was still a horcrux.
Rory didn't kill Nagini because he wanted Neville Longbottom to have the chance to kill the snake, since he knew very well what it was like to be an underestimated badass. He didn't destroy the diary for the same reason - the Sword of Gryffindor would have to be imbued with basilisk venom for Neville to be able to kill the snake.
He then went to deal with the locket. He'd put some thought into destroying this horcrux, since it was better protected than the others. Voldemort was a powerful wizard; he knew that the potion in the basin would hurt him a little, although far less than it would hurt anyone who was not as badass as he was. Therefore, he asked a house elf who had once given him a hand moving the Pandorica to accompany him. He knew that a house elf would be able to get out of the cavern, while anyone else who was not as awesome as Rory would not be able to leave easily. After drinking the potion, he was overcome by thoughts of Amy, so he gave the house elf, Kreacher, the locket, and told him to leave and destroy it, before apparating back to the Pandorica. He left a note for Voldemort with a fake horcrux: the Dark Lord would never have forgotten the name of the muggle (or so Voldemort thought) who had punched him so hard in the face. Rory knew that until the day Voldemort was finally defeated for good, the Dark Lord would hate the name of Roranicus Awesomenus Britannicus as much as that of Dumbledore or Potter. He was so preoccupied with Amy hat he forgot to check up on Kreacher, but since he knew that Ron Weasley would destroy the horcrux, he wasn t worried.
He knew he wouldn't get to see Harry destroy Voldemort, as that would happen after Amy was born (so if the Doctor was able to control his time travel for once, Rory would be gone by then), but he didn't mind. However, he didn t want to upset the timeline, so in 1990, before Harry Potter had even started at Hogwarts, he got on a very specific train and used legilimency to put the idea of Harry Potter into J.K. Rowling s head, so that the first book would be published in 1997, just like he remembered.