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 one of four, Misty is sent on missions to obtain items of great importance to Opaline’s plans. However, she finds herself questioning her place as Opaline’s protégé more and more. Meanwhile, Sunset and Starlight are called to the cutie map, only to find themselves abducted by it and being deposited in the future.