The people of the girl-themed Sistar System turn out to not be evil at all; they just simply tried too hard to establish friendly relations with the people of Apocalypsburg due to a poor understanding of each other's behaviors. The real villain turns out to be Rex Dangervest, who manipulates Emmet into destroying the Sistar System, which also ends up destroying all the Lego worlds in the event known as "Ourmomageddon" (in the real world, Finn and his sister Bianca have fought so much that their mom makes them put away all of their Lego models). And during this incident, Wyldstyle/Lucy ends up becoming briefly aware of the real world like Emmet did in the first movie.
But by far the most shocking twist of all was the true identity of Rex Dangervest: he's actually Emmet from the future, all tough and "grown-up" like all his friends had wanted him to be. He became that way because when he originally set out to save his friends, he ended up lost under the dryer and no one ever tried to find him, so after being isolated for so long, he adopted his tougher persona and built his spaceship out of various time machines to gather his raptor forces and then seek revenge against the friends he thought had abandoned him. (In hindsight, the clues for this twist should have been very obvious in some of Rex's physical details, but I had originally assumed it was all part of the gag of them having the same voice actor.) And of course, after the final battle to restore the Lego worlds and Emmet declares he will never become like Rex, Rex simply fades away like in Back to the Future (though he has enough time to appreciate Emmet making a better choice than he did).
