Five years after the events of the movie Star Trek: Nemesis (Stardate: 61812.5), the enterprise crew is heading towards their rendezvous with Captain Jean-Luc Picard's Ex-Commander, Riker's, ship to create a peace treaty with the Romulans. On the way, however, they discover some turbulence which forces them to crash land on an unknown planet. Once there, they find pieces of Data who got blown up when destroying the Scimitar (events that occurred in Nemesis). When the away team transports back to the ship, Data is somehow all back to normal and fully functional.
In Equestria, Twilight was writing a letter to the princess when Pinkie Pie arrives at her door inviting her to come to Gummy's 2nd birthday party. Twilight accepts and soon the rest of the Mane 6 arrive at Twilight's place. A strange fog comes in and soon an earthquake occurs. Princess Celestia landed near them to warn them that even though they defeated Discord, reminents of his chaos still remained. They couldn't do anything to stop it other than not create any dis-harmony, as it could make it worse, and possibly awaken Discord once more. Immediately, they all go looking for the Cutie Mark Crusaders and find them, arguing, right next to the statue of Discord.

Picard's next step was to promote Data to his new Commander. By sacrificing himself to save him, the Enterprise, and possibly the entire Alpha-Quadrent, made him more human that any of them. Q suddenly appears on the main screen and shows them the ponies and informs them of how they're soon going to meet each other.

As the CMC continued fighting, they accidentally bumped into the statue of Discord, causing it to break his imprisonment and escape. Princess Celestia goes off for the elements of harmony and the Mane 6 fend him off while she does so. To their surprise, they find out that Discord, in fact, is not the one behind the chaos remainding.

Q opens up a wormhole straight in front of the enterprise and starts sucking them in. They tried to navigate away but make no progress. When Princess Celestia return to the ponies, she informs them that a giant wormhole had appeared near the castle in Canterlot and that they would have to investigate. Little by little the Enterprise was heading closer and closer to the wormhole. Once the ponies arrived in Canterlot, they all saw the huge wormhole, and there was a disk-like object sticking out and coming through it. Little by little, it came out and crashed into Celestia's castle.

The ponies ran to the top floor of the castle where the Enterprise had landed. They couldn't see inside but the crew inside could see them. Nothing was making sense for the Enterprise crew. How could they have landed in a world of fictional cartoon ponies!? Rainbow Dash found a way to get in but finds out it's blocked by a glass-looking surface. She gets prepared for a Sonic Rainboom but ends up going even faster after making the Sonic Rainboom after only half way down. By now, most of the Enterprise crew were in sickbay but the bridge crew got into the turbo lift and started heading to the bridge. Meanwhile, the ponies were entering the Enterprise from the outside into the bridge. They looked around when they heard the doors open and saw the humans coming out. After conversing introductions, Q appeared and took Discord with him. Soon, Admiral Janeway contacts Picard and informs him that Benjamin Sisko, who Picard had some relations with (like killing his wife as a Borg called Locutus and introducing him to Deep Space Nine), had been captured and taken to Equestria. Now all that was left was to find him.

After searching in a few locations in Equestria, Janeway contacted Picard again saying that Sisko was in a forest north of where they were. That's when Fluttershy informed them that that happened to be the creepy and spooky Everfree forest. When they arrived there, they met Zecora who led them to where she had found Sisko. Soon Discord appears and tells them that he actually had been spying on Q because no one could create chaos in Equestria except him. He woke Sisko up from his unconscious state and opened a portal to the past. There would be no way to defeat Q now so the only way to do that would be to go back in time and stop the Enterprise from going through the wormhole. Janeway transports there to help them out. Q, however, appears, and makes the portal disappear. Discord makes it reappear and they go off on a series of appearing and disappearing wormholes until one time, their powers collide creating the portal to crack and break, creating a disruption in the space-time continum and they all fall unconscious.

Everyone wakes up somewhere mysterious. They were in Ponyland (the location of which the show My Little Pony Tales takes place) where they meet Starlight and her friends. After discussing how to go back, the unicorns begin using their magic and the Starfleet officers use their phasers at their horns, creating more power large enough to bring them to the present. After going through the portal, however, they find out that they, in fact, did not make it to the present and actually came about five minutes before they left. They find themselves talking to Zecora. Once Q appeared to stop Discord, the future ponies jumped out to stop them from creating a time anomaly. However, by doing so, they themselves create a paradox forcing themselves to be erased from existence and the entire space-time continuum to collapse on itself, causing it to re-expand in the exact same fashion up until the point where it all started: Q.

Pinkie invites Twilight to her party when the others arrive while Picard promoted Data. After the events from the first few chapters happen and Discord awakens, Q decides that maybe it's time he gives them a chance and increases the power of the elements of harmony to seal away Discord for good. Q also gives the Enterprise crew a chance but giving the Romulans an idea for peace. Picard bid farewell to his good friend Riker and the ponies began partying at Pinkie's party. In unison, both Twilight and Picard say "I wonder what adventure awaits us next."