The protomolecule is an infectious agent of extrasolar origin, first discovered on Phoebe by the Martian Congressional Republic in 2342. It has the ability to radically alter infected life forms and utilize their biomass in various ways.
Not a life-form in itself, the protomolecule is described by Antony Dresden as "a set of free-floating instructions designed to adapt to and guide other replicating systems". It is able to maintain and adapt its primary structure in a wide variety of conditions, and it has an affinity for carbon and silicon structures, but is likely anaerobic and will not degrade upon exposure to oxygen. Naomi Nagata identified the substance aboard the Anubis as a "nano-fluid", revealing that the protomolecule is some form of nanotechnology, essentially functioning as a pseudo-biological "computers". As molecular nanomachines, the protomolecule uses ionizing radiation as an energy source. Its growth significantly accelerates if it is exposed to high doses of ionizing radiation, and it depends only on the abundance of such energy.
The Protomolecule was sent by an alien civilization inside an interstellar asteroid 2 billion years ago. This asteroïd was captured by Saturn's gravity to become one of its many moons we called Phoebe. Yet its intended destination was Earth. It is initially seen as a weapon since infected humans die.
the Protomolecule is not a weapon but a tool. It functions as an advanced pre-programmed platform created by the Ring Builders. The programming appears to be using alien worlds' biomass (with a preference to reproductive systems, i.e, life) to build things. Therefore, life doesn't "die" but is rather transformed.
Not a weapon, the Protomolecule turns out to be an incredibly flexible tool, capable of creating and functioning in and as a variety of purposes and objects, as we learn new ones every step throughout the series. In rudimentary terms, the Protomolecule could be described as an all-purpose real life hacking code that rewrites whatever it touches to suit its own ends.
The Protomolecule samples sent to the stars 2 billion years ago were panspermia-like molecular phages, invented and developed for massive galaxy exploration. Like the phages we know, it could only become active when it came into contact with a replication mechanism. On Earth, then primitive life would have provide enough to feed its impressive transformation process, hijacking any life or inanimate to nurture a mysterious growth. Yet the Protomolecule was not programmed to develop life. Its first goal is to create the infrastructure needed for interstellar travel and communication. Once it grows with enough biomass, it moves to the outer limits of the targeted stellar system and builds a gate. It leads to a wormhole establishing a connection to its creators' galactic-wide Ring Network, a network of more than a thousand of other gates, opened on as many stellar systems. In our world, for example, it was bound to create the Sol Ring, our gate to access the whole network.
Another important use to the ancient aliens who created it is to develop suitable facilities on planets (power plants, data storage, fixing shops etc). Even milleniums later, it activates their technology, like a fuel, somehow magically awakening drones, ship-reparing platforms, transportation lines, access to virtual libraries and so on in the many worlds behind the Ring Network gates.
The Protomolecule has a complex relationship with human brains. At times after its release, humans discover several ways it has to guide, impact or divert individual consciousness but when absorbing living matter, the protomolecule, however, is not conscious. That's why it is a tool and not a form of alien life.
At some point between the Bracewell probe swarm launch and the present day, the civilization that invented and then scattered the protomolecule was attacked and seemingly destroyed by an as-yet-unidentified aggressor.
In 2342, the MCR landed on Saturn's ice moon Phoebe to survey it for ice mining. When core samples from the moon were investigated, however, silicate samples were found, and the Martian government approached Protogen corporation from Earth as a co-sponsor of a long-term research facility. Protogen discovered the alien agent, dubbed it "the protomolecule", and began experimenting with it. Later, Protogen killed all Martian scientists on the Phoebe station to hide their discovery, but the goal of this killing is unclear. There are suspicions that Phoebe was likely first limited to laboratory scale protomolecule experiment developed as an initial identification of protomolecule properties/capabilities in action. Testing on living entities is a strong evidence of MCRN long term supremacy strategy to develop a weaponry against Earth.
The samples of the protomolecule were placed in a safe onboard the Anubis to be taken to another location. On the way, the Anubis would board the Scopuli and take prisoners to infect. This would get out of control, however, when the entire crew and prisoners became infected by the protomolecule. The second, maybe even more likely scenario is that Scopuli was a lifeboat for some Belters personnel inluding Julie Mao, who escaped from Phoebe Station when Protogen launched its first protomolecular experiment. When it became clear that some eyewitnesses survived, Anubis, with a sample of the original protomolecule on board, was ordered to destroy all other evidence of the Phoebe incident. Intentional or accidental, protomolecule infection killed crew members on both Scopuli and Anubis, but not Julie who was imprisoned in an isolated quarters after boarding.
Julie Mao survives taking the shuttle Anubis 1A to Eros. However, Julie was infected and eventually died at a hotel on Eros, where her body was found by the crew of the Rocinante and Detective Miller and later by a team of Protogen scientists led by Anthony Dresden. All subsequent samples of the protomolecule in the Sol System are just from Julie - patient-zero.
Having found the protomolecule sample extracted from the body of Julie Mao, Protogen was able to make second protomolecular larger scale test by using this sample to infect the population of Eros as a controlled experiment to study and observe how the protomolecule would behave when fed with 100,000 humans. Upon the infection beginning, signals were sent to Thoth Station where it was studied.
In 2351, the first major outbreak of the protomolecule, known as the Eros incident, took place. It was a controlled infection of the entire population of Eros, numbering one and a half million humans. With this amount of biomass, it was revealed that the protomolecule had the ability to create a hive mind of sorts, which integrated itself with the computer systems of Eros station.