One day our heroes were preparing to visit Kirk for his Birthday, but Twilight is still sad that Celestia, Barret, Luna, and Cadance are still trapped in Tartarus, but Shining Armor tells her that they'll get them out someday wich Twilight doubtfully agrees. Just then, Dudley showed up and explained that Kitty's gone! And Team Griffin/Eeveelution, Judy, Nick, Gabby, Ember, Peter, the guys, Little Bear, his friends, Doug, and Skeeter have been helping him too, but had no avail on finding her. Then Spike spurts out a letter and was written by Ernie (whom the Dazzlings, Diesel 10, Suri Polomare, Katty Katswell, and Tirek teamed up with), and the letter explains that he has Kitty in the future. And our heroes soon transport into the future. But with the villains on the other hand, Ernie explains that Kitty is a beautiful Jedi, and he corrupts Kitty! And he calls her "Darth Black Cat" and she accepts it.
Three years into its five year mission, the USS Enterprise arrives at Starbase Yorktown, a massive space station, for resupply and shore leave for her crew. Struggling to find continued meaning in the endless nature of their mission of exploration, Captain James T. Kirk has applied for a promotion to Vice Admiral and commanding officer of Yorktown. He recommends Spock as the new captain of the Enterprise. Meanwhile, Hikaru Sulu reunites with his family, Montgomery Scott works to keep the ship operational, and Spock and Nyota Uhura amicably end their relationship; Spock also receives word from New Vulcan that Ambassador Spock (Spock's future self from the original timeline) has died.
The Enterprise is dispatched on a rescue mission at short notice after an escape pod drifts out of a nearby uncharted nebula. The survivor, Kalara, claims her ship is stranded on Altamid, a planet within the nebula. The rescue turns into an ambush when the Enterprise is quickly torn apart by a massive swarm of small ships. Krall and his crew board the ship, and unsuccessfully search for a relic called the Abronath that Kirk had obtained for a failed diplomatic mission. Krall captures and removes many crew members from the ship. Kirk then orders the crew to abandon ship as the Enterprise's saucer section hurtles towards the planet.
On the planet's surface, Sulu, Uhura, Shining Armor, Blythe, Ember, and other survivors are captured by Krall. Meanwhile, Brian is on a different site, till he spots Kitty! Then she turns around and attacks him! Brian yells at her, till he sees the Sith eyes of her and he duels with Kitty, but was no match with her Force strength. Then Sylveon arrives and teleports them out and meets up with the others who had gathered up on the crash site, and Brian tells the others that Kitty has been corrupted by Ernie, and claims that they need to destroy him.
Kirk and navigator Pavel Chekov, accompanied by Kalara (whom our heroes catch up later), locate the wrecked saucer section. Kalara is discovered to be following Krall's orders when she tries to retrieve the Abronath. Then they see the corrupted Kitty Katswell trying to kill the others. To escape Krall's soldiers, Kirk activates the still-functional thrusters, causing the saucer to lurch forward, crushing Kalara. Meanwhile, a wounded Spock and Dr. Leonard McCoy search for other survivors. Spock confides to McCoy that he intends to leave Starfleet to continue the late Ambassador Spock's work on New Vulcan. Meanwhile, Scott is rescued by Jaylah, a scavenger who previously escaped Krall's encampment. She takes Scott to her makeshift home, the grounded USS Franklin, an early Starfleet vessel reported missing over a century earlier. Scott is reunited with Kirk, Chekov, McCoy and Spock. Using the ship as a base, they plot to raid Krall's camp and transport the crew to the Franklin (and Dudley manages to stun Kitty), then escape the planet in the repaired ship. And our heroes managed to turn Kitty back to the Light Side of the Force. Meanwhile, Krall coerces Ensign Syl to hand over the Abronath that she had kept hidden for Kirk, then dissolves her completely. The Abronath is the missing half of an ancient bioweapon, created by the planet's original inhabitants, which can disintegrate any humanoid. With the device complete, Krall intends to attack Yorktown and kill its inhabitants, and, using its advanced technology, go on to attack the Federation. Kirk and the others free the crew as Krall launches into space with the bioweapon, leading his drone fleet to Yorktown.
The Starfleet crew pursues Krall on the Franklin. Scott transports Spock and McCoy into one of Krall's "swarm" ships. They learn that VHF transmissions can disrupt Krall's communications. Matching the swarm's frequency and using the 'classical' song "Sabotage" by the Beastie Boys, they destroy almost the entire swarm. Krall and his three surviving ships crash in Yorktown. As Krall flees into the city, Uhura and Kirk discover from the Franklin's logs that he is actually Balthazar Edison, the former captain of the Franklin. A pre-Federation human soldier, Edison became disillusioned with the newly founded Federation, rejecting its principles of unity and cooperation with former enemies. When he and his crew were stranded on Altamid by a rogue wormhole, he believed the Federation had deliberately abandoned them. The three survivors prolonged their lives with the technology of the planet's extinct natives (at the cost of their human physiology and their numerous victims' lives), and repurposed their dormant drone workers into the swarm. Edison now plans to destroy the Federation and resume galactic conflict. Kirk pursues Edison into Yorktown's ventilation system, where Edison activates the bioweapon. Before it can be unleashed, Kirk ejects Edison and the bioweapon out of Yorktown, disintegrating him in space and leaving the weapon lost forever. Spock and McCoy save Kirk moments before he is also blown into open space.
Then the villains have our heroes cornered, and then in a bright flash of light the royals have returned! Tirek is shocked and dismayed, but decided to battle them with his magic regardless how the lightsabers can cut flesh. The royals accepted it and Barret, Belle, Jasmine, Anna, Elsa, and Judy decided to join in and they battle him, and then Ernie fights with Peter, and Adagio duels with Brian and Sylveon. Peter and Ernie fight in a docking bay, Ernie tries to hit Peter with a giant wrench but get caught in chains, and Peter throws a switch that makes him go up, and he goes up too. Meanwhile Brian and Adagio get a blade lock, but force pushes him to an edge but he grabs on. And before the siren can finish with him, Sylveon cuts off her arms and she screams in pain and Brian shoots her pendant and she dies. Meanwhile Peter is almost killed by Ernie, but Ernie is killed when Kitty activated her lightsaber and he fall down below, killing him for revenge of making her a Sith. During the battle with Tirek, the royals, and Judy are gaining the upper hand when Tirek blasts them all off of him and grabs Celestia by the throat and prepares to suck her magic dry when Belle jumps in the air and cuts off his horn making him unable to suck magic and he shrinks back to his older self, he pleads for mercy but Barret tells him that a villain like him deserves no mercy, and kills him with a DC-15A blaster. Diesel 10 prepares for a getaway but is knocked into a barge filled with sludge by Percy. Then Suri Polomare gets ready to duel Rarity, but before the duel Sweetie Belle tells her to stop, and convince her to come to the Light Side of the Force, but Suri refused and shoots her in the chest! Rarity takes her Lightsaber and clashes Suri's like crazy, but Suri Force push her down a pit, and kicks Rariry's Lightsaber down the pit. But Rarity jumps up and uses Sweetie Belle's Lightsaber and splits her in too! And as Suri falls, she shows her splitter body, and Aria and Sonata knowing their outnumbered surrendered and get put in chains. Everyone comes to Sweetie Belle, and Rarity weeps of her fallen sister, but she coughs that she is alive! Then Celestia gets a pain to her stomach witch makes our heroes confused, but they takes her to the hospital.
And at the hospital she gives birth to an alicorn filly, and she calls her "Sharon". And Barret tells our heroes that during their time in Tartarus, Celestia have been pregnant with a foal ever since they were kidnapped by Tirek. And our heroes were surprise, but were happy too. But Kitty feels down after she had try to kill her friends, but our heroes forgive her.
Commodore Paris closes the unsolved cases of the fate of Captain Edison and the USS Franklin crew. Kirk decides to remain as a captain, and Spock chooses to stay in Starfleet and resumes his relationship with Uhura. Jaylah has been accepted into Starfleet Academy based on Kirk's recommendation. As the crew celebrates Kirk's birthday, they view the construction of their new ship, USS Enterprise-A, and after its completion, they depart on their next mission.
- Princess Celestia, Princess Luna, Barret Barricade, Knockout, Puffer, Dolphy, Rachel, Mighty Joe, Daylight, Jenny, Pete, Kevin, Morley, Blitzer, Dile, Skarloey, Rheneas, Sir Handel, Peter Sam, Rusty, Duncan, Blythe Baxter, Zoe Trent, Pepper Clark, Penny Ling, Vinnie Terrio, Sunil Nevla, Minka Mark, Russell Ferguson, Mitzi, Buttercream Sunday, Sugar Sprinkles, July, Belle, Princess Jasmine, Princess Anna, Elsa the Snow Queen, Judy Hopps, Nick Wilde, Dudley Puppy, Kitty Katswell, Team Griffin/Eeveelution, Peter Griffin, Glenn Quagmire, Cleveland Brown, Joe Swanson, Little Bear, Duck, Cat, Owl, Emily, Lucy, Doug Funnie, and Skeeter Valentine guest star in this film.
- Ernie the Giant Chicken, The Dazzlings, Diesel 10, Suri Polomare, and Tirek will work for Krall in this film.
- Thomas & Friends: The Great Race, Zootopia, and Star Trek: Beyond were both released in 2016.
- This film will make the first appearance of Princess Sharon.