I have attempted to place canonical Equestrian history in chronological order.

This is not the order I think things should go in. It's the order, to the best of my ability to determine it, that things must go in (regardless of whether or not I like it.) It functions on simple pairwise determinations of the form "Ok, X needs to have happened before Y."

So we're talking about things like, "Young Starswirl stuff must have come before old Starswirl stuff," "A tree needs to be planted before it can be fully grown," "Things Luna did in places other than the surface of the moon about a thousand years before the show must have happened pre-Banishment," or, "Ponies had to go to the Everfree before they could put stuff there."

Things like that. Lots of things like that.

While what follows is irreverent and laced with profanity, it is a sincere attempt to use what canonically happens in the show to create a consistent chronology.

-- At least 2,000 years* before Friendship is Magic Grogar rules the backwater that would eventually become Equestria. He loses harder than any other villain has ever lost (hence the long banishment) because he couldn’t keep his bell from being stolen.
-- -- Cloudsdale is said to already exist at this point in time, but it is said in a children's book. Take it or leave it, reader's choice.
-- Nothing of note happens until within a pony-lifespan of 1111 years before School of Friendship is founded, except:
-- -- Ponies leave the lands that Grogar ruled and forget about them.
-- -- It is presumably during this period that ponies organize themselves, along racial lines, into the three tribes.
-- Tirek and Scorpan come to steal magic from ponies.  Scorpan comes to like ponies, self-reforms, befriends young Starswirl (the Bearded), alerts Celestia and Luna to Tirek’s plans, teams up with the two alicorns to (successfully) defeat Tirek, and goes home.
-- Starswirl, now older, becomes teacher to Celestia, Luna, and Clover (the Clever).  Why the first two need his lessons when they were taking on great evil back when he was a young wizard, who’s part in history didn’t even merit the use of his name, isn’t touched upon.
-- In response to Windigos making other lands uninhabitable, ponies seek new homelands. Each of the three tribes independently rediscover the lands once ruled by Grogar and decide to settle. After ponykind is almost obliterated, Equestria is founded.  Clever Clover plays a key role. Starswirl is off dicking about somewhere. We should not look down on him for this, because the Celestia and Luna are also MIA.
-- -- For the first time in (what was then) living memory, ponies come into contact with the Everfree Forest
-- Celestia starts to raise the sun, taking over for a group of unicorns that includes Starswirl, this happens 1111 years before The School of Friendship is founded.
-- The Sirens show up.  Stygian recognizes both that they need to be dealt with and that he can’t do it himself.  He forms the Pillars of Old Equestria; they defeat the Sirens.
-- Stygian wants to help his team, who are also his friends, in the field.  He tries to gain the strength to do so via a spell that uses a significant item from each of his friends.  He didn’t ask to borrow those items. His friends reject him; darkness welcomes him. He becomes the Pony of Shadows.
-- Starswirl assumes that Stygian is irredeemably evil and forms a plan to take out Stygian at the cost of the entire group of friends.
-- -- Since they’re going AWOL and feel mildly like maybe they shouldn’t leave everyone else hung out to dry, they plant a thingy.  It will one day become the Tree of Harmony
-- The plan to get rid of Sygian by getting rid of the whole group works like a charm.  The Pillars and the one who founded them are gone.
-- -- While the Pillars took up horticulture to mitigate the effect of their departure, they did not tell anyone what they were doing, so their disappearance was a complete mystery.  Celestia and Luna will spend over a thousand years wondering where the fuck Starswirl went.
-- Discord takes over Equestria.
-- Time passes.
-- Celestia and Luna learn of the Tree of Harmony (now grown into an actual tree) and the Elements it contains.  They find it, swipe the Elements, use them to defeat Discord, and don’t put them back when they’re done.
-- -- Discord was planting plunderseeds at the time of his defeat.
-- Celestia and Luna now rule Equestria.  Maybe.
-- Sombra happens.
-- -- The Crystal Empire suffers an existence failure. So too does Sombra.
-- Ponies think the night sucks.  Ponies have thought the night sucks for a long time.  Luna is getting sick of it. Yada, yada, yada, Nightmare Moon.
-- -- Princess Luna now resides on the moon.
-- -- Princess Celestia becomes sole ruler of Equestria.
-- -- Maybe it’s because she used them against a pony who was Bearer to three of them, maybe it’s because Harmony doesn’t function well as a solo act, maybe it’s something else, but whatever the reason, the Elements reject Celestia so hard that they change their shape and composition, except for one that seems to represent Harmony Magic, but is just called “Magic”.  That one flounces so very hard that it needs what amounts to a six pony ritual just to get it to exist again.
-- For a thousand years, nothing interesting happens.
-- -- Except Cadence becoming an alicorn, that’s interesting.
-- Nightmare Moon returns, she’s defeated by the restored Elements of Harmony.  For the first time each Element has its own Bearer. None of that “I’ll take three, you’ll take three” crap.
-- -- Celestia and the no-longer-Nightmare Luna return to ruling Equestria together. Cadence is somewhere doing something.
-- Discord comes back.  He’s defeated by the Elements of Harmony.
-- Chrysalis makes her debut. Unlike Discord, she keeps the Bearers away from the Elements, and is therefore not defeated by the Elements of Harmony.  She’s defeated by weaponized love.
-- The Crystal Empire, and Sombra with it, regains existence. The Crystal Empire sticks, Sombra not so much. Specifically, Cadence, the Crystal Heart, and the Crystal Ponies defeat Sombra with "light and love".
-- -- Cadence becomes Princess of the Crystal Empire.
-- Twilight ascends, gets her Element stolen, goes to another world where she allows it to be corrupted, and returns with her Element recovered.  Almost immediately, Harmony Magic, which had no problem keeping them in check for over a thousand years, fails to stop the plunderseeds from growing into plundervines, by which it proceeds to have its figurative ass kicked. The Elements are returned to the Tree; things go back to normal.
-- Tirek returns.  He gets beaten by the Tree of Harmony and, presumably, the Elements it contains. The Seedling Tree-Castle of Harmony is born.
-- Starlight Glimmer happens.
-- Flurry Heart happens.
-- Chrysalis has a really effective comeback tour, she is defeated by the power of Garish Colors.
-- Twilight Sparkle fanfillys her way into undoing Starswirl’s . . . whatever the fuck you call that.  (If it had gone as planned it would basically be murder by sextuple suicide; since it proved temporary instead, it wasn’t.)  Stygian is redeemed by the power of not offing one’s friends at the first sign of trouble.
-- Using a stick that once belonged to Scorpan and a very pissed off unicorn, the Storm King beats the princesses.  He is defeated by stupidity, duplicity, loyalty, and vengeance (in that order.)
-- The Seedling Tree-Castle of Harmony says, “Hey you racist assholes, don’t you think it’s about time that you recognized that non-ponies are people too?” The School of Friendship is founded.
-- The previously unknown Roots of Harmony are discovered when the Tree of Harmony takes up psychological torture as a hobby.
-- By exploiting the Roots of Harmony and the Tartarus Pen-Pal Program, Cozy Glow, who speaks of ponies as though she isn’t one (which no one ever looks into), drains the magic from Equestria in order to send it to another realm.  (No one looks into which realm she was sending it to, either.) She is defeated via Tirek’s buyer’s remorse and the fact that Psychological Torture Tree can be jump-started provided you’ve got six kids, each of a different species, to hook the jumper cables to.
-- Grogar comes back, resurrects Sombra, and summons Chrysalis, Tirek, and Cozy Glow.
-- Sombra takes over the Crystal Empire with little difficulty, appears to be defeated by the Elements of Harmony, and then destroys the Tree of Harmony and the Elements thereof (which had been his actual plan.)  The Seedling Tree-Castle of Harmony and the Roots of Harmony show no evidence of being affected. Sombra is defeated by the Element Bearers of Harmony, sans Elements.
-- Equestria gets a new Tree of Harmony.  A bigger one.
-- Chrysalis, Tirek, and Cozy Glow retrieve Grogar’s bell.  They don’t give it to him.
-- Season 9 ends, presumably this involves Grogar actually doing something for the first time in his life, but it doesn’t come out until next month, so I don't actually know. (I could find out, since other places have already gotten it, but I'm not going to.)

* The only thing we know for sure is that it was millennia before Season Nine. It takes more than one complete millennium to make millennia, so that's a bare minimum of 2,000 years.