For a Thread by Thread history, take a look in the category Threads.
The Very Short History
Ok, seriously, you want me to spell out 70 threads worth of history here? Ok, buck, I got this. Here we go.
This thread started in oat as a series of ridiculous and not at all serious events in /pony/ (now oat). In it we've been attacked by Bec Noir, Mobster Kingpin, Covenant, Crystal Ponies, a Computer Virus, Cthulhu powered Max, and so on in an oddball list of villains. The thread took its turn for the serious at around threads 24 or 25. Since then, Ponyville has been destroyed twice, once when caverns below it gave way and then during the fight with the Crystal Goddess Ninah while she was still insane. A shield tower was placed in the middle of Ponyville to protect it from more explosive blasts As things currently stand, Ponyville is still a rural town, but has some fresh sprawl on the edges. The Everfree is more dangerous then ever because of incursions by the Hedge, the realm of the Fae. It also got attacked again recently by a Computer Virus who attempted to infect the town.
Yea. This is missing a ton of information, but this is here just to get you up to speed enough that you can jump in. If you want (or need) to know more...
The 'Brief' History
Keep in mind that a LOT of stuff happens in these threads, and that even this longer format misses out of many details
A Brief History Lesson With Miss Inkwell (1-46)
“Alright, listen up, because we’re doing this my way and we’re doing it fast.
These threads started out as a refuge for the various Trolls about /oat/(Or, /pony/ as it was known at the time) The earliest topics were mostly just chit chat and the occasional battle with Bec Noir, our first recurring villain.
Around eight or nine someone prototyped Twilight Sparkle, causing the Twilight Noir/Jack Sparkle Incident. It should be noted that this was the first time Noir tried to attain power from Ponychan itself.(Something he would do many times in the future.)
After his defeat, the group was faced with yet ANOTHER villain, in the form of one Mobster Kingpin. He planned on using Nepeta’s vast imagination to conjure up the perfect bride, driving Nepeta insane in the process. This battle was unique in that it was required for the group to solve some pules before they could confront MK, FMK, DMK, and eventually DMMK. Eventually he was defeated, and Clubs Deuce attempted to use DMMK power to revive Bec Noir. But he was boo’d off the stage and only ever made cameo appearances.
A few threads later, an Image Derp that showed Pinkie Pie being attacked by a strange spider beast sparked the next major plotline. This had elements of the last which were more refined. Being a search it had a definite starting point, which was the establishment of the homeroom. While most of the group searched for Pinkie Pie, Vriska was captured and subsequently ‘killed’ by Furio Tigre(She got better). The “Boss Fight” of this plot was notoriously difficult to end, which sparked major arguments which will never be spoken of again. Needless to say, the Spider Queen was defeated, Pinkie’s fragile Psyche was twisted in ways we’ll never understand, and Adam got a nice new hat.
The next smaller plot picked up back at the homeroom, and around the outside of it. Gamzee, finding that he was no help to his friends while under the effects of sopor slime decided not to take it for awhile. Anyone who has read far enough into Homestuck knows how bad this is. Before he his finally subdued he damages his relationship with a few of the ponies. This seems to permanently have an effect on him, as he continues to wonder if he’s ever going to be any use. This has in fact rather effected how he used to not care about anything and be happy all day. Gamzee is now capable of having a sad.
On the start of the next plot, The Gentle Coltte introduced his Manor to the group, which became the next focal point. After a brief space adventure, and Miss Inkwell learning to hate Sollux, one group went down into the basement of the manor while another group tried to rescue Trixie from a fire. The tag team of Joey and Rainbow Dash easily solved the hedge-mae and rescued their friend, while the other group discovered something much more dangerous. Deep underground, far beneath the manor there was a mass tomb of human skeletons. Very odd, considering on this planet humans are few and far between. This led to a battle with the Polka-loving Skeleton King, who after taking too long to defeat, had the caverns collapsed on him by a sleepwalking Trixie. This did severe damage to the above Ponyville, and sunk the Gentle Coltte’s mansion. Miss Inkwell and Joey’s bodies were lost underground.
Rainbow Dash finds out about this and forces a rescue team together which leads to the discovery of the pure magic crystals. Trixie gets the deepest into the tunnels, following the call of the crystals to find a horribly injured Miss Inkwell and Gentle Coltte. They remain in the cavern for 3 in-game days before Eridan arrives to assist Trixie Miss Inkwell to a state in which they can be moved. Meanwhile the other group finds the Seeker, and asks of his secrets. This establishes how the world became a nexus for several universes. In the 3 days Trixie spends in the caverns, she gets to know the crystals, listens to their whispers, and an individual intelligence contacts her and persuades her into a specific task which will appear later. Eridan takes a crystal for himself, intrigued by its properties.
The Gentle Coltte soon discovers of Trixie’s use of the Crystals, and attempts to force a painful, life threatening operation on her to remove it from her body (Which had yet to be needed...(You shut up! It’ll become important!)). Trixie is enraged by his ungrateful attitude, her crystal having an effect of amplifying her emotions, but also acting as a voice of reason. She eventually calms herself down, and the crystal advances a stage in its development, merging with her. Eridan goes on a quest of self discovery, destroying a mountain while Trixie wallows in... whatever ponies wallow in for a while. With Miss Inkwell’s assistance she regains her composure, and uses a spell she learned from the crystals to teleport out of the Gentle Coltte’s boarding house where she was being held, saving an exhausted Eridan in the process.
Else where more characters were awakening, specifically Ryu, the dragon god of many forms and Freya, the Demi-goddess.. Daughter of the Goddess? Goddess child? Daughter of the Goddess of the Crystal ponies. The Crystal ponies, are in fact, the creatures that have been speaking to Trixie, and they tell her that the Goddess is going to be summoned again. The Goddess had long ago been corrupted by the touch of the impure, and needs to be stopped. Good thing there just happens to be a group of heroes in the area. Meanwhile Max notices his toys of power have been stolen, and uses one of the remaining ones to turn into a pony, in pursuit. It would appear that Gamzee was the one who stumbled upon those toys, and quickly makes friends with the ventriloquist dummy, Charlie Ho-tep.
Either way, The Gentle Coltte was not amused with this tomfoolery, and called in his Comrades the Gentlemen to investigate the outbreak of Pure Magic. Mr.Gr’uhnd, Mr.G’lxsph and Mr. Rulek arrive promptly to put a stop to this madness, fighting alongside the normal assortment of heroes. Meanwhile Max, now calling himself Matt, is experiencing a strange personality change. Eventually, it is revealed that Matt is a completely different entity than Max.
Either way, the battle against the goddess is underway. Gamzee uses his Toys of Power to the team’s advantage, and this catches the eye of Mr. Gru’uhnd. He is obsessed with keeping balance, and those toys are VERY illegal due to their rampant power. He decides to quietly steal one of them though, for his own reasons.
Soon, through the combined efforts of the Crystal Ponies, Our Heroes, and the Gentlemanly backup, the Goddess is defeated, and Freya takes her place as mother to the Crystal ponies. It seemed that there would be no rest, as Mr.Gru’uhnd, as he promised earlier, demands that the culprits, including Matt, Trixie, Freya and Gamzee, are arrested. It is not so easily done, however, and Mr.Gru’uhnd is forced to withdraw when met with resistance. He vows to return.”
“And that’s the farther reaching parts of the story. Get out of my class room now. Except you Gamzee, you’re staying after with me.”
Letter to the Princess (47-64)
Dear Princess Celestia,
I'm afraid I'll have to begin this in apology. I should have been a more diligent student. I guess I've just been busy with everything that has been happening here in Ponyville. This would probably go smoother if I finally gave you some sort of explanation to what all is happening here.
Ponyville ended up being constructed over two very important factors in all of this mess. The first is an Alien Facility whose purpose was experimental. In its past, it held a massive 'drive' that enabled the facility to try and move a whole planet. This failed, placing Equestria where it is long before any pony of our kind roamed the world. This failure has done a massive amount of damage to the barriers separating different dimensions.
On top of this, Ponyville was built over focal point of magic. A nexus. This focal point on top of the facility has caused high energy points that seem to momentarily allow other dimensions to breach into ours. This has caused a lot of beings from many other worlds to appear here. This has been both a wonderful and dangerous experience.
Wonderful because I've gotten to make a wider variety of friends then I could have ever imagined existed. I've learned of a dozen other cultures. I've even learned about the subject of 'Apiculture,' which is one part 'computer science' (which is also a new science I learned about), one part biology, and one part agriculture. The number of things that we've learned about in these past two weeks is unfathomable.
This leads me back to the facility, and onto the subject of dangers. The facility I mentioned, for example, contacted its home dimension and brought in two waring parties, one of which was threatening to destroy the land around Ponyville just to dig up the occupant of the facility known as 'the Seeker.' On top of that, an older race that existed before the facility was built rose again. A race known as the loe'athal. They are... Symbiotic with ponies, at various levels.
When it reawoke in the resulting collapse of the original Ponyville, it awoke an angry Goddess, maddened by thousands upon thousands of years of imprisonment. One of the other people who arrived through the nexus, another god had even sworn fealty to her. It resulted in a large scale battle to stop the gods from forcing the loe'athal on everypony. We barely won that fight.
The surviving God, Jormungandr, is adamant on bringing the loe'athal to everypony. He also loved his Goddess. In trying to protect this planet, he was willing to work with the aliens in their attempts to annihilate another species from their own dimension. He was willing to do anything to get the Seeker. And anything to get the Goddess back.
I can't really say either people are 'good' people. We had another confrontation with him. One that was lost. He went out of his way to try and disassemble somepony at the very core against their will for his love. He didn't end them, but... I don't feel it was right. He resurrected the Goddess. She seems only intent on exploring for now, but it is something critical to warn you about.
I can feel them now, battling again. I hear it in the loe'athal. These gods and demi-gods are lost and angry. I'm can only hope we all get a moments respite from the constant fighting.
I guess I should also include an apology. I'm sure you've since gotten reports on what I did to the Equestrian Army. Yes, I borrowed part of it to build an actual combat force. It was... Necessary. With all the threats we've been facing.
Thankfully, one of the Trolls somehow managed to get the aliens to leave, their portal closing behind them.
We need to schedule time to talk. We need to talk about these events personally. You probably want to talk to me about the Equestria Defense Force, and I need to talk to you about Mr. Rhys. Give me a good time to meet, and I'll be there.
Always your Faithful Student, ~ Twilight Sparkle
PS: I also did not cover the Gentlemen, from of which Gru’uhnd WILL return, bringing havoc with him. I also fail to cover more of the Hedge's encroachment into Equestria due to Matthew.