Unobtanium is a remarkable substance discovered on board a defeated alien ship. Once a way was found to harness it, the new power it provided allowed humanity to leave its own 'back yard' and venture out into deep space. The substance is not only a source of fuel, however, it also has a positive effect on the development of 'beings' that come into contact with it, sometimes accelerating their evolution. It's the reason more super-powered children are born on the Heroships than would normally be expected.

Unobtanium used in the ships engines leaves behind small extremely valuable particles of dust as a by-product. This is collected by the Arch and is used as in-game currenccy.

Quote from the Official Forum

In-game, Unobtanium is a far-trans-uranic material (atomic number in the hundreds) with multiple isotopes. This is completely possible in science. This is also an important part of the backstory. The material used to power the engine generators aboard the Justice is one particular mix of Unobtanium isotopes. This mix was chosen because the by-product radiation is particularly helpful and positive to humans, while also giving good fuel effectiveness. The byproduct radiation from this mix is not positive to other life forms, especially if the life did not originate on Earth, which is why they tend to mutate into hostile new species. In addition, the Unobtanium isotope mixture used to power enemy ships is different than ours, so when we humans raid other ships we have a slight disadvantage…we are a tiny bit weaker and our enemies are a tiny bit stronger.

Hence it would be an enormous win for an enemy species like the Nagdellians if they could seize one of humanity's few heroships and change the engine mix to benefit them, and then replace the humans with Nagdellians. Such a conquest would be strategically huge in the galactic balance of power.