This story is a sequel to Twilight Sparkle Becomes a Changeling Queen, Book 1

Twilight Sparkle is a changeling queen. She has found herself back at the old hive, with old memories... and new opportunities. She brings a new, more pony perspective to changeling problems; and she's very excited to experiment at finding new solutions with the help of her willing and eager subjects.

But some things do not change. A queen must also defend her subjects from any who would do them harm...

Set after season three.

This story is a sequel to The Freeport Venture

Young Kukri Doo faces the greatest crisis of her young life. Worse than the time her ship was chased by pirates. Worse than the time the Equestrian Intelligence Service took her prisoner. Even worse than the time a Primal Changeling tried to turn her into its next meal.

It's Sunset Shimmer's birthday!!! And despite being the Shimmer-mare's personal apprentice, Kukri doesn't have the first clue where to get the perfect gift for her or what that gift even is! Her parents and friends simply fail to grasp the gravity of this unfolding crisis, or the terrible consequences of failure. Who can imagine what horrors might be unleashed if Kukri can't find the perfect present before time runs out?!

After the Friendship Games, Sunset feels it's time to return home.

Only when she gets there, Twilight's castle is nowhere to be found, Cadance just got her horn, and Princess Celestia is still calling the bacon-haired pony her prized student rather than a failed one. And just reliving her past isn't on the table thanks to a pair of wings Sunset seems to have sprouted upon her return to Equestria.

With Sunset being back before she's supposed to, will the world stay as harmonious and on track, or will everything go down in flames as Sunset has to deal with allegations that she's really a changeling in disguise, a nerdy stallion with blue hair that wants to be her coltfriend, a pretty pink princess in need of remedial magic lessons, and an annoying purple pre-teen pony that will absolutely not go to bed without first being read Starswirl's Complete Mystical Mysteries Compendium?

Only time will tell

This story is a sequel to Dusk's Dangerous Game

Twilight Sparkle, known to all but the three Goddesses as Lady Everstar, the Evening Sage, has ruled over her kingdom for nearly five centuries with all the wisdom and grace of which she is capable. Her lands are wild and exciting, the prospects good for those with brilliant minds and daring hearts. But now something has changed in the Evening Kingdom, something has changed the balance of power so profoundly that even Twilight herself cannot tell how events may unfold.

Across the ocean, an ancient evil is stirring, its dark hunger can finally be realized. Its servants are many, brutal, and cunning. They are found among the lowest of lows, and the highest of highs. With the balance of power so disrupted, it is at last time for their shadowy plans to come to fruition, to cast off the darkness and strike against the night.

It will take the power of goddesses, magic both familiar and ancient, and the most unlikely of heroes to save not only the Evening Kingdom, not only Equestria, but the entirety of Creation as we know it.

Sequel to Lines and Webs and Dusk's Dangerous Game. Knowledge of the previous stories is not needed, but reading them is, of course, encouraged.

Followed by Courts of The Magi.

This story is a sequel to Second Princess of the Night

With Twilight and Ruby Sparkle settling into their new positions as rulers, they oversee the transition of the bat ponies to their new home. But now that two of the Four Shepherds have appeared, Equestria must prepare itself for the rest. The next Shepherd will be unlike Sombra or Night Walker, as he threatens not only Equestria, but the kingdoms of the other races as well. Awakening from his mysterious slumber, he will carve his way across the land, intent on regathering his unwilling army. But before he manages to travel to the edges of the world, he will leave a parting gift in his wake to Rainbow Dash and four other ponies he chanced upon. With her life forever changed, Rainbow Dash prepares herself for her new fate, as well as finding her place among the ponies that share her future.

Twilight Sparkle was merely trying to go out to lunch with her number one assistant after a long morning in the lab when a strange dome of energy passed over them. Now on the other side, with Spike missing, no one in Ponyville recognizing her and certain facts about the town and Equestria she had taken for granted changed, Twilight has some questions.
What happened?
Where is she?
How can she get back?
And perhaps most importantly:
Who is this "Champion of Princess Celestia, Sunset Shimmer Defender of the Realm" everpony keeps going on about?

This story is set in season 3, before Magical Mystery Cure. All other episodes have occurred, or are not relevant.
Characters who deserve to be on the main character list have been removed to prevent spoilers.
Edit: Updated to teen upon reflection of the fact that it is going to get rather violent latter on.
Cover art by the fantastic Lord-Giampietro of deviant art. http://lord-giampietro.deviantart.com/

After accidentally creating a weapon of mass destruction, Twilight is forced to confront a choice she made long ago in order to assist the war effort and a secret military order.

This story is a sequel to Freeport Venture: More Equal than Others

Sunset Shimmer had grand ambitions upon becoming Freeport's only magus, most importantly helping out the citizens of Freeport itself. When she hears of an outlying farming community in danger from a horde of undead, she knows she has to help them. Even if they can't pay her fees, it's the right thing to do.

However, this new challenge might be too much for her to handle. These zombies are unlike anything she's ever seen, and an old enemy is mixed up in the middle of all of this. Sunset has no idea what dark secrets the undead horde hides, or the danger posed by the necromancer behind it.

Twilight has always been the best there is at magic. She's won dozens of scholarly competitions and tests of skill in Canterlot. But when it comes to the more violent uses for magic, she is essentially clueless.

When she meets a strange unicorn in a seedy bar, he introduces her to a little known sport that will test her knowledge of magic in different ways. That is, of course, if Twilight can't resist its primal lure.

Midnight Sparkle appears one last time in Twilight's dream, not to antagonize her, rather to just talk and clear things up.