Marking the Generations is a reimagining of the later stages of the Make your Mark series. Follow the adventures of Sunny, Hitch, Izzy, Zipp and Pipp as they make a new friend in Misty and meet two ponies from a past generation.

Twilight Sparkle has always done her best for Equestria. As her reign finally ends, she realises her final decision to safeguard Equestria will have consequences. However, let it not be said that Twilight Sparkle ever left Equestria to its own devices.
Calling on Starlight Glimmer and Sunset Shimmer. She transports them through time to assist the new generation to identify the Elements of Unity and defeat the evil she was unable to alone.

In part two of four, our heroes return to the Brighthouse with information they hope will heal both Starlight and Sparky. Then, there is trouble ahoof as Peach Fizz and Glory suddenly go missing. Their disappearance being strangely connected to Misty’s dreams. Will our heroes unravel the mystery of Misty's dreams in time to find them?
Also, what of Opaline now she's lost her Protégé? Are her plans to take over Equestria now on hold for good?
Then, why is Sunny having so many problems with her powers? Will she be able to resolve them or are they lost forever?