Heavy spoilers

Warning: heavy engame spoilers ahead.

The game plot has three layers. First, there is the publicly known ship records that the heroes take from the net and that are freely available at the start of the game. Second information source is their own experience with the aliens and other bits and pieces they learn throughout the game. Thirdly, there are hints about alien problems and goals, mostly at the end of the game, with partial and a bit contradictory information revealed in the different game endings and the rest left for the player to hypothesize and fill in. This page hosts ideas about the third layer.

• Alien backstory: they could never directly, effectively communicate with humans, because of brain/notions/language differences. Forcibly turning humans into alien-human hybrids would not work, either, as there is no dialogue between the competing parts of the organism and eventually they would become fully aliens, with no understanding of humans. So, the aliens tweak the medical bay so that it very slowly changes the human brain into an alien brain (and the rest of the body, to a lesser extent, mostly the nervous and hormonal systems). The humans are free, unaware, striving to survive, adapting to the new fighter personalities, so it works. There is a lot of dialogue between their older selves and their new way of thinking, feeling and reacting. They remain human by relating to each other in the squad and communicating with the outside world. The aliens fight them hard enough to force them to use the bay often, but not as much as to kill them off. There is still a real risk of death, because it has to be realistic and the humans are to progress and eventually succeed, to keep them on growing as fighters, tacticians and alien behaviour scholars. They will also start using alien equipment in time, a feat which was unattainable for any captured humans to date and which will speed up the transformation. Even if heroes learn about the trick at some point, they will still fight the aliens, because they count on outsmarting and eradicating the aliens eventually and being their own masters, with alien technology in their exclusive, of all humanity, disposal. They would hope the aliens underestimated them.
• Since aliens are very different, we will never know nor understand their plans after the Contact and their motives for Contact, for risking their and human life for Contact, for forcing Contact instead of manifesting their presence, leaving a puzzle and flying off (probably too long trip back, though, so they have to stay, but they might just hide). A bit about aliens will be shown in how heroes change, e.g., how they become more ruthless, less emotional, more logical, intelligent, perhaps with a kind of holistic intuition. But we will never know if parts of it are less what aliens are, and more a semblance of the alien computers taking part in the process or reflection of what kind of transformed humans aliens need for their plan or just a result of a long fight for life, killing, alienation.
• Let HP and stats increase very slowly in the ship's medical bay (and gym), if XP allows. XP represents raw muscle mass increase and sensory-motor experience and the gym/bay refines, hardens, orders and makes permanent the improvement of muscles, nervous system, memory, reflexes. A bit of steroids+, too, but raw strength is less important than coordination and harmony. The bay also gradually reduces any genetic, developmental and after-illness faults and underdevelopment. Aliens improve that aspect of the medical bay, because they don't want the heroes to die by chance from stupid physical limitations, and healthy body eases changing the brain, the nervous and hormonal systems. Let the medical bay improve the understanding of alien motives, the ability to hear aliens, perceive their stats, etc. This second effect won't be easily noticeable, because it shows only much later on the battlefield. The first effect can be explained away by the medical removing latent health problems of heroes and by their organisms adapting to the punishment. Let them also enjoy using the bay, be very cheerful, let it be a bit addictive and feel a bit wierd, too. They've heard about such advanced healing and rejuvenating medical equipment before, but they could never afford it, so they can't compare it with the real best human technology and they are happy to use it.
• A complementary wild idea, perhaps depending on the player actions, is that at some point the heroes fail to evade authorities, get tired of evading them, or even consciously choose to lure them in. The aliens slaughter a couple of consecutive police and army raids and the heroes get the weapons, push aliens back, gain some alien weapons and get stronger. An option at this point might be to start space piracy. In time the aliens may even occasionally help against the authorities, as if by chance. In time the player starts questioning the sincerity of the heroes' and aliens' commitment to kill each other. In time the heroes may try to take over the solar system, using the alien technology, after killing off the aliens, or by cooperating with them, more and more skillfully. Anyway, the heroes are more and more alienated as the game progresses, first physically, because they can't leave the ship, then because they have a secret that can cost them everything, then because they gain knowledge of things the rest of humanity does not even suspect, then because they start thinking differently and understand more of reality and at last, because they realize they are not 100% homo sapiens any more (and they don't complain).