Emperor Mateus was brainwashed by Zemus
He was Zemus' first attempt at getting someone to gather the crystals. Unfortunately, he didn't count on Mateus' thirst for power. Then he heard about KluYa's sons, and decided to try and brainwash one of them, figuring they'd be easier to control being half-Lunarian.
Guy doesn't speak beaver. He hit his head escaping Fynn.
In fact, I'm not sure we shouldn't leave him behind to get some vocational help.
The city of Mysidia and Ricard Highwind the Dragoon is one bit. His son being named "Kain" in Dawn of Souls is another. In the DS version of FF 4
Kain states that his father died while fighting an empire, and even mentions that his father's name was Ricard.
Well, the population sure had fun reshaping the land and creating new kingdoms after the Cyclone and the rise of Pandemonium.
This brings to...
He disagreed with Zemus' plan to kill all humans and leave the world for Lunarians. Like Kluya, Mateus wanted humans to reach the level of Lunarians, but he preffered a faster way, an easier way, which leads him to The Dark Side
. Mateus decided to make humans live the way of Lunarians, but to do this he first needed to control them, so he launched a coup in the strongest nation, becoming the new emperor of Palamecia. With that new political power in his hands, together with demons he summoned (from the Hell, mentioned by Rubicante in FF 4
), Mateus started conquering other nations. Zemus was out of play during these events: he was busy subduing Golbez and the Elemental Lords to his will.
Then, of course, Mateus is killed by main characters, but his Lunarian way of dying is a bit different than one would expect from a man, as he leaves something behind. And, like Kluya left a presence to turn his child into a Paladin, and like Zemus left Zeromus, a creature of pure hatred, Mateus left two sides of his personality. One, representing his power-hungry and human-hating qualities became the Dark Emperor, who rised Pandemonium from Hell itself and unleashed demons, wanting to destroy humans. Other, showing his pre-evil Lunarian self becomes the Light Emperor, asking dead humans to forgive him and essentially taking over the whole celestial chain of the planet. That doesn't go well, of course...
In his dying breath, the Light Emperor scolds humans for being hateful war-hungry fools, who will never leave their wars behind them, creating a prophesy for FF 4
wars of Baron. To clear the mess created by Mateus, Eidolons and the Elemental Lords reshaped the land and stayed as the world's guardians, answering only to the Summoners, with Odin becoming the king of Baron, the new strongest kingdom, created on the ashes of Palamecian Empire, serving as the defender of peace between mortal kingdoms. Alas, under Zemus' influence, the Elemental Lords re-populated a big portion of the world with monsters and undead, which would later become a part of Golbez's army. Eventually Cagnazzo "kills" Odin and disguises himself as the king of Baron, starting new wars against other kingdoms, which leads to Final Fantasy IV
At the end of II, the world is devastated, first by the Dreadnought, then by the cyclone, and afterwards by Pandaemonium. This is the War of the Magi. We don't see the Espers' part because they were used by the Empire, and the rebels never learned about them.
Quite plausible, if one looks in the library in Mysidia, there's a book that predicts machines will bring about the end of the world. The empire utilizes Magitek Armor, the same empire Kefka was directly involved in which led to the end of the world.