In an alternate world where everything and everyone is made of Lego, the Equestria Girls of Canterlot City's LEGO Team are forced to flee when an alien army known as the Changelings suddenly invade their home city.

Forced into hiding, the girls must rely on any assistance they can get, from an old friend from Equestria, to a team of ninjas, and even possibly one of the Changelings who desires a change of heart for his kind. But as a result of loose Equestrian Magic, Queen Chrysalis, ruthless leader of the Changelings, has obtained a special advantage.

When facing off against a shapeshifting army from outer space, their struggles will take them to distant places they could have never imagined. What exactly are the Changelings and their queen hoping to achieve? Can the Equestria Girls succeed against their greatest foe yet, or will they have finally met their match?