Penguin UFO (first boss). It is a component of the Metalwork Station, which is needed to craft the Starmap Upgrade MK2, which is used to get to the Beta Sector. The molten core looks like a metal canteen filled with lava.
The Molten Core is necassary to reach the Beta Sector and obtain better ores. So it would appear that you have to defeat the boss of each Sector to reach the next Sector, almost like levels.
Note: The Penguin boss will always drop 5 Molten cores.
Note: The Metalwork Station only requires 1 Molten core.