I'm mainly creating this topic as I wanted a place to discuss the events that lead to Gen 5 happening. I won't lie that I'm not the biggest fan of Gen 5 so far, but I am increasingly increased in how Gen 4 and 5 are connected, and the events that took place between the two.
So far, from what I can piece together from what I've seen (and correct me if I miss something):
According to Discord, there was a Unicorn that started spreading havoc across Equestria due to her "false ideals of a perfect Equestria". She managed to somehow separate every pony and I assume other species into abandoning their thoughts of equality, leading to fighting. I assume this Unicorn is Opaline. This then lead to what Discord describes as "truly terrible things" happening that lead to Equestria becoming more divided. It was only when Twilight eventually stored all the magic in the three crystals that there was harmony in Equestria again.
Sunny's version of the story seems to be a lot more simplified likely due to time. She describes the last part of Discord's story where Twilight stored the magic away into three crystals to keep the harmony. Though Sunny claims that after this, all the races decided to separate. She mentions that an Earth Pony got hurt by a Unicorn. This could be anyone but I again assume the Unicorn is Opaline.
Twilight's message I'm assuming seems to tell us about those "truly terrible things" that happened which Discord mentions. She's clearly talking about Opaline attempting to steal all the magic, to which she stores all the magic within the crystals to stop her.
That is everything I gathered so far. Each story kinda lines up but there are clearly some important details missing. The main thing that seems to be missing is what happened that lead to each pony separating after the magic was stored away into the crystals. The way Discord tells the story, it seems like everything was good after the magic was stored away and harmony was back again, but clearly something happened after that.
As I'm writing this, I also realise that its likely that Opaline was the Unicorn who eventually turned herself into a Alicorn by stealing magic. She then possibly went on some soft of rampage that lead to Twilight having to store the magic away and banish her. I feel like Twilight's decision to store the magic away likely came after many years of chaos. She likely did it to prevent anypony from ever using magic against each other. That's just a theory though.
I also avoided Misty's story as its clear that her story is a twisted version told by Opaline.