Twilight Sparkle and her fellow Elements of Harmony have faced down supernatural foes of the highest order, but sometimes the deadliest danger can come from places one would least expect. As Twilight is forced to bear a devastating secret, her efforts to keep the Elements together may well tear them all apart.
The plotline of the thrilling Pony Psychology Series continues with an exploration of deception, despair and Discord.
This series takes place between Season Two and Season Three.
Secrets and Lies shares the Pony Psychology Series TVTropes page.

When Scootaloo moves to Ponyville, she meets a certain cyan pegasus who becomes her idol. Things go well until a pivotal event causes her hopes and dreams to come crashing down around her. Broken and betrayed, Scootaloo must learn to accept her reality and embrace her inner strength with the help of her father and two best friends.

[Now with a super awesome reading by Neighrator Pony.]
[This story's sequel can be found here.]

Cloud Kicker might just have the wildest life of any pony in Equestria. Marvel at the insanity that is her life, and laugh at the suffering of her poor beleaguered best friend, Blossomforth. And maybe, just maybe, there's more to her than just the lovable sex maniac everypony thinks she is.

This is a semi-sequel to "The Incredibly Dense Mind of Rainbow Dash." Not really a proper sequel, since it's focused on Cloud Kicker and Blossomforth instead of Rainbow and Pinkie, but it's in the same continuity. So I guess that makes it a follow-up-side-quel story. Or something. You don't need to have read "The Incredibly Dense Mind of Rainbow Dash" to read or enjoy this, but you ought to read it anyway, just because.

TvTropes Page

The central story of the Winningverse.

We got a tag for Cloud Kicker, but Blossomforth still deserves one too.

Twilight Sparkle has a lot of difficulty getting a good night's sleep. She has to keep it a secret from the ponies who care about her, because they might disown her. Worse, they might try to help...

WARNING: The first five or so chapters are, on reflection, properly grimdark. If this makes you run away like a puppy that just laid a brown egg on the new carpet, that's your prerogative entirely. Please don't tell me that I'm objectionable for having written it, though, because that's not very nice. Or accurate. At all.

The shiny new art is a commission by this lovely person, so do feel free to check her out for all your creepy-pony needs.