Pre-S1:

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S1 part 1: Part 1 takes place over 4 months. Starting with ToFL. In Part 1; Twilight's herd is found out, and with Royalty being part of a forbidden love affair Equestria is split in two. Philosophically speaking. One part embracing their forbidden love, and some of them coming out in the open. The flames of their forbidden love fanned by Twilight getting ousted.

The other group outraged in the openess Twilight and others take their forbidden love. Seeing it as a corruption and evil taking route in Equestria. Cadance and Fleur De Lis become rulers of Equestria in Celestia and Luna's stead. With Twilight still being the third Princess, regardless of her abdication of the throne being demanded by the anti-Forbidden Love groups.

Part 1, follows the fallout of that.

TOFL

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Part 2: [planned]

Part 2 opens with something strange going on. This is the start of the Changeling Invasion of Ponyville, They get found out when a Proto-Queen tries to act like Sweetie Belle, findout the Forbidden Love groups of Ponyville had members of their love group taken.

Twilight is in her first trimester of pregnancy, she doesn't know if it's changeling or Sweetie that's the father. Other canon pregnancies are Diamond Tiara with Filthy Rich's child, and Derpy with Dinky's child.

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Part 3:

The hunt for the changeling hive begins. Takes them across Equestria [3 months], second trimester happens with pregnant ponies. They come across information where the hive is, and those pregnant come to terms that they have to sit back and protect their families future, rather than act in the present.

The anti-groups band together to form The Purification of Equestria. Makes waves across Equestria as they see that even the "true rulers of Equestria" are wrapped up in depravity and evil ways.

Ends with the showdown between Chrysalis and the Forbidden Love ponies.