The Machina are an intelligent race of machines that were originally from the Mechonis. Unlike the Mechon, which are more the equivalent to the non-sapient animals and monsters of Bionis, the Machina are a peaceful, intelligent race who were unfortunately mostly destroyed by the ancient battle between the Mechonis and the Bionis.
Machina, unlike the races of Bionis, do not require sustenance to power themselves the same way the organic species do. Their life energy is directly drawn from the ether around them, instead. All they really need to survive is fresh water. This means that Machina can live exceptionally long lives with some being many thousands of years old.
Most of the remaining Machina are content to let bygones be bygones and continue existing in a hidden village on the Fallen Arm; the literal disembodied arm of the Mechonis that was severed during its battle with the Bionis and lies somewhere between the two colossi. However, Egil (the son of the Machina elder Miqol) has dedicated his life to eliminating all life on the Bionis in order to stop a similar event from ever happening again. He is the sole driving force behind the Mechon attacks and the creation of the Faced Mechon.
Role in the Story
No-one on Bionis, with the exception of Dickson, is aware of the Machina; they had believed that all Mechon are mindless automatons that simply devour and destroy the life on Bionis during intermittent attack waves. Shulk first meets the Machina when he awakens alongside Fiora on the Fallen Arm, having dropped from the crumbling Galahad Fortress several miles above after the party's first run-in with Egil. Though initially suspicious of any mechanical lifeforms, he and the rest of the party are brought into the Hidden Village and meet the many peaceful Machina citizens there. There's also even a few Homs that ended up there after falling off during the war.
Miqol, the village elder and leader of the few Machina that are left, explains the history of his people and what Egil is doing and why, though he disagrees with his path of vengeance. He also reveals that he is Egil's father. He implores Shulk to find some way of stopping him, including killing him. Shulk decides to find a path that won't result in Egil's death, despite all the bloodshed he has caused.
Later, after Egil activates the Mechonis and the team is forced to escape before the entire colossus starts moving again, Miqol and the other Machina help them back to Agniratha: the old Machina capital inside the Mechonis. They do this by activating "Junks", a mobile airship that had been masquerading as a structure in the hidden village. Though the group stops Egil, Zamza is able to awaken and activates the Bionis. His first act in the newly awoken Bionis is to annihilate most of what's left of Mechonis. The Machina are able to survive the onslaught by moving Junks to the lake in Colony 6 and helping the people there hold back the Telethia swarm. In the new world, the Machina continue to live among the Homs, Nopon and remaining High Entia peacefully.