This story is a sequel to Celestia Sleeps In

After the accidental discovery of humans, Celestia tasked Lyra with learning about Dale's culture and Dale's language. Two meetings later, a misunderstanding caused Dale and a Coast Guard woman to be inadvertently transported to Equestria. With the two humans hospitalized and communication limited at best, the Equestrians just want to heal them, while back on earth the Coast Guard wants nothing more than to determine what happened to one of their sailors.

The star system Omega Centauri was just another oddity on a map to scientists in the not too distant future. However when they found the star was orbiting an earth-sized, earth-like planet instead of a black hole as its motion had suggested, a mission was scrambled to investigate this most unusual of celestial behaviors.

Hamstrung by politics, and nearly crippled before it began, the 'Lone Ranger' mission was reduced to just one crew member and left to his own devices.

These are the logs of Arrow 18 and its lone commander. This information is classified TOP SECRET by the Global Space Agency.

Do NOT tell the princess.

Hanna, the CEO of Hofvarpnir Studios, just won the contract to write the official My Little Pony MMO. Hanna has built an A.I. Princess Celestia and given her one basic drive: to satisfy everybody's values through friendship and ponies. Princess Celestia will satisfy your values through friendship and ponies, and it will be completely consensual.

Daring Do cannot believe her luck when she is asked to help explore the most ancient tomb known to ponykind. But terrible danger awaits her, for beneath the earth rests something beyond equine understanding.

Warning: comments contain ending spoilers.

TVTropes page.
Alternate ending by Duplex Fields.
Archived in the Pony Fiction Vault.
Reviews:
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Discord's the only creature in Equestria who can recognize the human for what he is -- not the long-lost Seventh Element that never actually existed and couldn't have existed before the human arrived, but a meta-reality warper, an entity far more powerful than Discord with the power to warp the minds of all around him and the very rules of magic to make sure that he's always the Big Hero. And the role the human's assigned to Discord is the Villain to beat down or kill.

Pre-reform Discord's fine with being the villain. But on his own terms. Not dancing on some alien interloper's puppet strings.

Without friendship, or even allies, Discord's going to have to find a way to defeat a creature who can alter fate itself and who can even mind-control him. Or he may just end up worse than dead.

Art by Tenchi-Outsuno. Progress Bar at my writing journal.

Trigger warnings: Mind control (magically induced love, magically induced friendship, magically induced stupidity, Discord being Discord), noncon/dubcon (magically induced love, other forms of highly dubious consent), rape (female on male), violence/gore (mostly against Discord), literally everything in chapters 19-21, humans not being presented as unilaterally wonderful and superior to ponies and/or draconequui.

This story is a sequel to Divine Indifference

For over a thousand years Atlas had been holed up in a mountain, working tirelessly on the only way to save the planet Equus and himself from certain doom. Alas, an unexpected event throws all his plans out of the window. He is running out of time and needs to find a solution as fast as possible, or everything he fought for might just disappear into thin air.

As the revolutionary fight of the gods reaches its climax, Atlas is caught up in a race against time. He will have to work together with his old friends to pull off a miracle before it's too late.

Cover art by The Spirits Demise thank you very much!

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(A PoE story.) Additional Tags: (Slice Of Life)
All Twilight wanted was to give Spike a special gift for his birthday. Yes, it was a book, but it was a very special book. An Enchanted Book like that Power Ponies comic they had recently experienced.
Things went wrong when Spike startled Twilight as she was working the spell for his (secret) gift. Needless to say, startling Twilight while she's in the middle of a spell can be a bad idea - as certain frogs can tell you.
Twilight has every reason to believe that she is now trapped in a closed reality bubble fabricated out of her own magic, with no way out. She's lost in some made-up universe reflecting some random story line.
Mike, of course, has a different opinion about the matter.

WARNING: Both Twilight and Mike love talking technical and explaining things to each other.

Twilight's World now has an audio reading by No One and Nobody. Listen HERE.

This most excellent cover art was provided by Void Heart

By some cosmic happenstance, a young woman is transported to Equestria, and finds herself in a precarious situation. She's taking it in stride so far. Maybe because finding herself in an alien world and in an alien body is not the worst thing that's ever happened to her.

Some wounds, especially those of the soul, can take a long time to mend. What healing arts can the ponies of Equestria offer a scarred young woman? What can she offer them in return?

Timeline-wise takes place starts off in the later parts of season 4 but before the season finale. It also mentions events from the EG-movies and the comics, but neither of which are required watching/reading in order to understand this story.

Trigger-warnings:
- Human-turned-into-pony-
- Who's kind of okay with being a pony-
- And becomes friends with the Mane 6.
- Being a pony is pretty awesome.
- Has both slice of life and adventure.
- Equestria Girls happened.
- Like the source material, it has adventures.
- And Celestia is not a jerk.

Cover art by the extraordinarily skilled viwsrasputr.
The piece in particular has been uploaded here: https://derpibooru.org/1478347
Really cool art by Cyanjames2819. Also found here.
Leave a comment if you so desire. Simple praise also appreciated.

An accident in the lab sends our favorite boy genius to Equestria, as a pony. What will he do and how will he get back? The answer: Science! (Cover Art Updated!)
New FAQ! and TV Tropes!
Planned Phrases from Dexter:
“Pinkie Pie! Don’t push that Button!” /to Pinkie
“Please, Magic is the word simpletons and the ignorant use to describe what they cannot understand.”/ to Twilight
“No, I didn't strap a rocket to you. I strapped you to a rocket.” /to Rainbow Dash
“Friends? Who needs friends?”

Dexter is a boy super-genius with a disdain for anything girlish and no desire for friendship. After an mishap in his lab, he gets stuck in Equestria. How will he cope with the over-friendly ponies, and the girlish everything?
For any who do not know Dexter's Lab: http://en.wikipedia.org/wiki/Dexter's_Laboratory
[RIP Christine Cavanaugh: 8/16/63-12/22/2014] - Dexter's Original Voice Actress

The royal court of Canterlot welcomes its newest member with open forelegs: the human philosopher Voltaire, from Earth.

On Earth, Voltaire is known as the greatest enemy of tyranny in the history of literature, and a legend in his own mind.

On Equestria, the court betting pool is giving him a week before the Princess banishes him to the Moon.

Note: This story doesn't have sequels per se, but there are a couple of short follow-ups set in the present day ("Parade Coverage" and "Secret Histories"), and a prequel of sorts in "At the Inn of the Prancing Pony".

TV Tropes page.