I haven’t seen all episodes of Season 2 yet, so I may be off topic completely here. But I just came up with one, actually two, ideas about the motives of the ancient race that is responsible for creating the protomolecule and the wormhole network spanning space (that I read about internet spoilers already). I also don’t know the books.
many billion years ago one of the many early life forms that evolved on young planets made it against all odds and became a a god-like species wielding unbelievable technology. They were obviously masters of genetic engineering and pretty likely found ways to prolong their own lifespan and defy sickness and other problems that organic lifeforms suffer from. They traveled to the stars, visited many worlds all over the galaxy, maybe many hundred galaxies (still only a tiny fraction of the expanding universe). They tried it all, helped younger lifeforms evolve, tinkered with them (often failing, sometimes creating new wonders), they tried to make contact with more advanced species and they watched them grow. In the end, they found, that all life must end some day. Evolution is competition. It’s wonders are only a sideproduct of the constant struggle for domination. But total domination leads to evolutinary stasis and then decline. They also found, that artificial intelligence is not the solution for them. They wanted to preserve the wonder of life, the one oddity in a vast cold universe that would one day end in a fireball or become an eternal dark grave. While developing the protomolecule as a tool to create their tunnel network, they had to decide between two choices: continue what they did for millions of years until another species would sooner or later take their place, risking that all forms of life would extinguish themselves in the struggle – or convert all life in the universe into a form, that would last.
What if they used the protomolecule to become the catalyst or template for all lifeforms it encountered, skipping the million years of evolution each encountered lifeform still has ahead of them, and turning them into the desired lasting lifeform by making „a copy“ of that species, but with all the necessary traits and abilities of the ancient race. An experiment that would put all lifeforms encountered on the same level in very short time. The goal is not to create a galaxy spanning empire or something like that, but to ensure that life will never be extinguished from the universe. The universe is not a friendly place for life. It is very very unlikely that life can evolve and become a higher intelligence, let alone something like the ancient builder race, in this universe. There are a myriad of very likely reasons why any form of life following the principles of evolution is going to get extinguished sooner or later.
The mystic protomolecule is a magic key to change this. Artificial light, a cure against the smallpox, an atomic bomb or crusie missile, or a jet fighter would have been considered pure magic by our forefathers, even only 150 years ago. It is unclear how a molecule alone could make all this happen, but we have to believe that the ancient builders found a way. The protomolecule is their heritage to the universe, they willingly gave up their own physical existence or they were wiped out eventually by their own predicted reasons. No form of naturally evolved life can last forever. Only the protomolecule could, with the potential to transform remaining minor lifeforms into the intended higher form of life again – forever. The proto-race created by that seeding and catalyzing method would probably not be human at all. It could look like anything, not even resemblign anything we know already or are able to think of.
The wormhole network would ensure, that the eternal lifeforms would always have means to reach each other, regardless of large the universe would become. The wormholes have no dimensions that relay to the real universe. They have no length, the do not get „longer“ as the universe expands, the time required to travel through them always stays the same. Thus, the ancient builders have created a universe within the universe. Only a re-contracting universe would endanger that concept and finally destroy everything in a terminal singularity. I guess the builders did bet on an ever expanding universe, though. In the very far future, only the proto-race would populate the wormhole network, which would be a cold and dark place, bereft of all energy. That’s the only problem this concept has, the protomolecule requires energy of some form (heat, electricity) to evolve. We don’t know if it requires energy continualy to exist after it has evolved into a higher lifeform, it is unlikely that it would not require any energy on a higher form of existence. Therefore, their survival would be connected to the remaining amounts of energy within their reach. After a while, no stars, no energy would remain within the expanding universe, everything would be stretched out over vast distances, individual electrons or protons would be seperated by many light years. We can’t say what would happen to black holes or to dark matter in such a dying universe.
I don’t know if this theory has major logical problems, it is very likely it does. Reading a lot of sci-fi I often encounter the seeder motif but with no real explanation about the goal of that behaviour. Advanced species create, change and destroy minor species on other planets. The only explanation we typically get is – they are advanced aliens, we are not able to understand their motivations. In Odyssee 2001 they unknown builders of the black monument gate had the same intention, but made the final error: they thought their advanced state of evolution and technology would make them safe. Humans found their graveyard millions of years later. My theory is, that (intelligent) life has only one dominating motivation – survival. A very advanced species would understand that higher evolution means an increase of risking total termination, not less risk. The only solution is to consistently take out all the parameters that make life prone to that. It is unlikely that all the myriads of protomolecule seeds they did send out will get destroyed or never hit a planet with lower lifeforms. They have struck the spark, that would always rekindle the fire someplace in this life-defying universe for all time, until that very universe would cease to exist.