The different groups of ponies leave the shop, with all except Twilight fitted with different gadgets from John’s arsenal, for their destined locations. When John and his gang arrive in the Crystal Empire, it has gone back into its original state of dictatorship when Sombra was in power over a thousand years ago. As the group of ponies begin to make their way to the castle, they encounter a group of three guard ponies sent by Sombra to interrogate them. They demand to know where Twilight Sparkle is, but the group refuses, so the guards charge at the friends. They knock them down easily, then make their way to the castle, which is now covered in dark spikes. Upon entering the castle, King Sombra mocks them for being late, but fails to hide his shock when he sees Starlight turned against him. Enraged by her betrayal, he and some brainwashed guards lunge at them, and a great battle ensues.
Meanwhile, the Mane 6 sneak into Canterlot and move stealthily through the night towards the palace. They come across random groups of changelings, which they easily navigate around as not to arouse any suspicion. When they reach the castle, they find Queen Chrysalis sitting in the throne room while her minions tend to her like a god. When she sees Twilight in her new form, she initially believes that Princess Celestia escaped; when Twilight reveals her true identity, however, Chrysalis laughs and mocks that they cannot stop her. Rainbow Dash, hearing a challenge, becomes eager to deliver, and she fires a few shots form her Gatling hoof, which hit the Changelings closest to Chrysalis. Together, the Mane 6 charge at Chrysalis and the Changelings, who form up and try to keep the friends from defeating them.
After a brief conflict, Chrysalis, fearing that she will be overrun, teleports out of the castle to somewhere unknown to the Mane 6, leaving the Changelings no other choice but to flee. The friends, led by Twilight, hurry down to the dungeon, where they find the Princesses collapsed on the floor of their cells, weakened from exhaustion. Princess Cadence is the first to wake when the Mane 6 enter the hallway and becomes overjoyed upon their arrival; hearing this commotion, Luna wakes up and greets the ponies warmly. Princess Celestia, however, remains unconscious on the floor; while Pinkie Pie and Rainbow Dash search for the keys, Twilight asks what happened to Celestia.
"When she returned from seeing you," Cadence explains, "Chrysalis had found out and was waiting here to 'teach her a lesson'."
Shocked and enraged by the news, Twilight lets her anger get the better of her and blasts each of the doors wide open with her newfound magical powers. Surprised by the sudden display of power, everypony stares at Twilight, including Rainbow and Pinkie, who just returned from their search. Cadence and Luna comment on Twilight’s new appearance, but she does not hear them as she rushes into Celesita’s cell and tries to wake her up. Finally, she coughs dryly and peers up at Twilight and smiles.
“I . . knew . . you could . . do it,” she musters before lying back down. Realizing the severity of the princess’ conditions, Twilight tells Fluttershy and Spike to tend to and watch over them, to which she agrees, and the rest of the Mane 6 leave to track down Tirek and Chrysalis.
In the Crystal Empire, things are a different story; John and his gang manage to force Sombra out of the castle as he flees from the scene, but he makes the train derail before teleporting out of the area. With their quickest mode of transportation eliminated, the group wavers its options; Jacob suggests that they teleport to wherever the others could be, but when Emily tries to teleport them, she falls over, exhausted from the previous battle.
"Can you try?" Jenna asks Starlight.
"Admittedly I have never practiced full teleportation, and I don't not want to risk sending us off-course," Starlight Glimmer explains.
"I agree," John says, "And even if we could teleport, there's no way we know for sure where the rest of them are now and whether or not they're in the middle of a battle. We should fly, it's the safest way."
"But that will take hours, time they might not have!" Jacob exclaims.
"Can you see any other options?" John asks.
"Well . . . ." Jacob considers the possibilities, "I guess not. Lead the way, and hurry!"
So, John, Jenna, and Jacob carry Starlight and Emily all the way back to Ponyville, praying that they are not too late to help their friends.
At Twilight’s castle, Tirek continues to destroy everything inside, including the Golden Oaks chandelier and the throne room, as he takes his full revenge on the castle. Soon, however, both Sombra and Chrysalis arrive at the base of the castle and demand to speak with him at once. He comes down and listens as they talk about what happened to “their” kingdoms.
“You said they wouldn’t fight back this time around,” Queen Chrysalis screams in anger.
“We didn’t sign up for this, Lord Tirek,” Sombra agrees, “We agreed to help you get revenge and have our kingdoms back, nothing more!”
Tirek, however, merely chuckles, “You really thought that they would just give up? No, they’re fighters, alright, and if you want to keep your freedom, I suggest you both finish the job and find them before they become more powerful than us!” Just then, the villains hear Twilight’s voice shout “TIREK!” and he smiles, “Looks like we won’t have to look very far,” he says as she strides out of the castle, with Chrysalis and Sombra following close behind.
The Mane 6 stand in the path leading up to the castle from Ponyville, their faces glowing determination; “Well, what do we have here?” Tirek roars, “Come to meet your maker again, Princess Twilight?”
“That’s where you’re wrong Tirek. It’s your time to fall!” Twilight shouts back, “Equestria has had enough of your tyranny!”
“I guess we’ll just have to see, then, which of us deserves to live or die,” Tirek growls as Chrysalis calls out for her minions to formation; suddenly, a giant army of Changelings appears in front of the villains, and she orders them to charge. Slightly intimidated by the sheer size of the Changeling army, Twilight musters the courage to get her friends on the attack, and soon an all-out brawl ensues, one of the largest in recorded Equestrian history.