What happens in these factories is anyone's guess. Apparently they make robots, as Canti is a Medical Mechanica robot and so are the many other robots he fights with in FLCL. Haruko's attempts to get Atomsk results in her pulling lots of Medical Mechanica robots out of Naota's head, as she turned his head into a dimensional portal she can pull things out of.
The 'Medical' part of the title was partially explained when Canti displayed his ability to take X-rays, but why most, if not all, of the robots are huge and violent is not clear nor explained. What is explained, however, is that Medical Mechanica eventually uses the 'iron' factories to iron out the surfaces of the planets they are put on, as Commander Amarao puts it, "Ironing out the wrinkles in your brain so you can't think." This may be a reference to the fact that "smooth brains" have lower surface area and are incapable of complex thought. Only innate feature of cognitive ability remain (Koalas for instance have "smooth brains" and are unable to eat eucalyptus leaves on a plate in front of them and can only eat when plucking the leaves directly from the tree). It could be that Medical Mechanica wants to eliminate free will to reduce the threats posed by sentient life forms. Commander Amarao implies that the government is in contact with Medical Mechanica which could indicate that Medical Mechanica only uses the irons in places that have proven to be erratic.
In FLCL Progressive, Haruko and Jinyu actually enter a Medical Mechanica facility to destroy the device Hidomi's headphones get power from. The facility is lacking in any kind of security this time, unlike Haruko's first time entering one. The interior is a white cylinder with light blue accents and has a spiral staircase recessed into the walls. These stairs surround a cyan column resembling a spine which connects to a silver robot's torso. The wall surrounding this robot is a hemisphere with pink-to-orange ombre designs resembling brain wrinkles. Medical Mechanica's irons are also shown to be incredibly strong weapons beyond just flattening surfaces. After being flipped to an upright position and attacked by Tonkichi's mech, it is revealed that the irons regenerate after being damaged and can retaliate via laser when in this position. The laser is long range and not particularly accurate, but creates explosions with enough power to negate that weakness.
In FLCL Alternative, Medical Mechanica is setting up a series of giant pins around the Earth, similar to the ones seen on map applications, seemingly only with the intention to create stronger robots for destruction at first. However, it becomes apparent as time passes that the organization is sending them meticulously from space to eventually evenly cover Earth's surface. This appears to be for increasing production of robots worldwide to be better prepared when their enemies enter any given sector. In episode 6, the Bureau of Interstellar Immigration realizes their true intention to finally smooth out Earth's wrinkles using the irons and pins dotting the planet. The process begins in Kana's town when an iron starts moving toward a pin, flattening the surface as it goes, but the protagonist uses her N.O. to teleport the iron away via a space-time rift known by the Bureau as the Naked Focal Point. It is unknown if this stopped the entire plan or simply protected Kana's town, but it is worth noting that one iron redirected itself towards Kana when detecting Atomsk's power in her N.O. channel, making it possible that all the other irons had their programming interrupted as well. They also use robotic models similar to Canti to protect the irons, though they lack the connection to Atomsk that allowed Canti's programming to be altered.
- Commander Amarao mentions in Full Swing that there is a connection between the government and Medical Mechanica, though later on he states that Medical Mechanica is just as bad as Haruko is and wants to destroy all thought across the galaxy.
- In Brittle Bullet, Commander Amarao states that Medical Mechanica sites from different planets send robots simply to destroy Haruko and Atomsk through Naota's head, implying that Haruko really is a Space Patrol Officer, and a deadly one.
- It is never explained how or why they captured Atomsk, though it may be assumed that he did not agree with their plans to iron out all thought and he tried to stop them.
- Medical Mechanica buildings have no entrances or exits, which may imply that they use N.O. channels to transfer things in and out of the facilities.
- In the anime series, Medical Mechanica could be considered the main antagonist.