Just a quick lies! outline of the overall direction of the series that I was seeing.

The School of Friendship: The Series is meant to take place across the Junior Year for the Student Six. It begins after "The Ending of the End", specifically about three months later as Fall begins. At the start of the series, Twilight has ascended and is now the Princess of Equestria, Starlight Glimmer is Headmare, Sunburst is Vice-Headmare, and Trixie is School Counselor. However Applejack, Rarity, Rainbow Dash, Pinkie Pie, and Fluttershy are all still teachers at the school at the start of the school year, although it'll be perfectly fine if we decide that some or all of them would rather move on and instead we bring in replacement teachers.

The first major event of the series, kicking off the season opener, is Twilight's decision to release Cozy Glow, Chrysalis, and Tirek from stone, and specifically to our interests have Cozy Glow once more enrolled in the School of Friendship, this time to try and genuinely teach her friendship. Since her true nature is known to just about the entire school body, and all of its faculty, Cozy Glow's ability to actually do damage around the school is pretty limited. The Student Six are at the start given a "project" of trying to reform Cozy Glow, something that they may resent and Cozy certainly does.

Chrysalis is remanded back into changeling custody and will spend the series at the Hive. Tirek I have no concrete plans for; he may be returned to Tartaros, or he may be sent back to the centaur lands. We can work that out.

The other major ongoing arc of the series is the slow awakening of Lavan. Lavan is an ancient monster of earth and fire, a huge tortoise that burns anything that can be burned and then eats the ash. He's not malicious, merely hungry, but he's also massively destructive. He last roamed the land 999 years ago but was defeated and driven into slumber by dragons, including a very young Torch before he became Dragon Lord (Lavan is the reason why the Dragon Lands look the way they do, although this works out for the dragons as they actually like it that way). Over the following millennium Lavan has become much more myth than fact, with most dragons who took part in defeating him having passed away and Torch having downplayed Lavan's threat in order to make himself look more awesome.

Throughout the Fall Semester (the first 13 episodes), Cozy Glow should remain primarily an antagonist. The Cozy Glow arc is intended to make two major steps forward: in "The Menace of Mane-iac", Cozy Glow is kidnapped by the comic book villain come to life, but will take an active role in defeating her instead of running away or aiding her; and in "Parent-Teacher Day", where she fully commits to trying to make herself into a better pony.

Lavan is slumbering for most of the season, but the fire tortoise does have two major build-up episodes as well: "Lavan the Dream", wherein Smolder and one of the other Student Six have to do a shared class project on an ancient legend and they choose Lavan (to introduce the idea of him), and "Stirrings", where Smolder and another Student Six (could be the same a "Lavan the Dream") take a brief vacation to the Dragon Lands but find themselves endangered by massive volcanic erruptions that are being caused by Lavan slowly waking up.

The two arcs will collide as Cozy Glow gradually learns about Lavan and, in the series finale, goes to the Dragon Lands, ostensibly to wake him up fully and take control of him, although in reality her motives should be presented as having been more benign. For one reason or another the Mane-6, Pillars, Princesses, and anyone else who could deal with the problem is indisposed, and so when Lavan wakes up fully it will fall to the Student Six to save the day.