Ok, so here's what I think is going on.
Dresden is a scientist that is somehow connected to Jules Mao, who, we know, is a huge businessman on Earth.
At some point, on Phoebe, they discovered or made something called "the Protomolocule." Dresden referred to this as a "revelation." The Protomolocule appears to be the black and glowing blue stuff on Julie and in the Anubis's core, and Dresden said "we can only learn by letting it learn." Mao approved moving forward with the "operation."
The operation appears to be outfitting Eros station with surveillance equipment and "science gear." They hired a bunch of the gangsters and criminals from all over the Belt, and shipped out most of the legit police officers and moved in the thugs. We know they faked a radiation leak by blowing up a ship, and herded everyone into fallout shelters. However, when Holden and Miller broke into one of the shelters, they found everyone extremely sick and getting hit with "industrial levels" of radiation. They are deliberately infecting everyone with the protomolocule, in order to study it. The end result of this is a whole superstructure of the protomolocule stuff, with working limbs of some sort, and manifestations of people-shapes using light motes.
Mao is a military contractor, and used that connection in order to get ships with stealth drives built at the Bush Naval Yards. Those stealth drives were stolen from Mars by Frank DeGraff, who was later killed in order to cover it up by UN Undersecretary Sadaviir Erinwright.
Julie Mao, daughter of Jules, rebelled against her father, and has spent years in the Belt fighting for Belter rights. This led to her getting hooked up with the OPA, the Outer Planets Alliance, a group that likes to think of themselves as a government, but is considered a terrorist organization by both Earth and Mars.
Julie somehow finds out about her father developing a new "Bio Weapon," and is sent on a mission to intercept it as it's transported between Phoebe and Eros. This "bio weapon" would be the protomolocule, likely on its way to Eros for the operation they'd already set up. The ship they were intercepting was the Anubis, and they were flying in the Scopulii. When the Scopulii tried to intercept the Anubis, thinking it a science ship, they were surprised to find that it was a gun ship, and were forcefully boarded. Something had obviously gone wrong with the containment of the protomolocule on the Anubis, since the scientist woman in charge of the Anubis was coughing, like we saw people infected with the protomolocule doing later.
Julie is thrown into a closet on the Anubis, likely because she's Jules' daughter. The crew of the Anubis set up a distress beacon on the Scopulii, and the mining vessel the Canterberry recorded it.
James Holden, Amos Burton, Naomi Nagata, and Alex Kamal, along with Shed Garvey, are sent in a drone ship to investigate the Scopulii, but while they are on the Scopulii, the Anubis comes out of cloaking and blows up the Canterberry, making it look like a Martian attack. The five survivors are rescued by the Mars Naval Flag Ship, the Donnager. While on the Donnager, Shed dies when the Anubis (or a ship like it, there appear to be six) attacks. The Donnager is destroyed, but Holden, Burton, Nagata, and Kamal are able to escape, along with full tactical readouts of the entire battle between the cloaked ships and the Donnager, on a gunship that they renamed the Rocinante. Though it appears as though they don't know that they have the tactical readouts.
The Roci takes an offer of safe haven from Fred Johnson, a leader of the OPA who also appears to have done something really really bad while a part of the United Nations military. Fred Johnson makes a deal with the crew of the Roci, where they were to follow a distress call put out by Lyonell Polanski, a fake name that Fred uses for his OPA operatives.
The crew of the Roci head to where the distress call was placed, and discover the crippled Anubis.
While Julie was in her closet, everyone on the Anubis appears to have died and become part of the mass of protomolocule gross in the power core of the ship. Julie broke out of the closet, discovered the protomolocule stuff, and sent out the Lyonell Polanski call, and then limped to Eros in an escape pod.
The Roci crew find the Anubis, discover the protomolocule stuff, and blow it the crap up. They follow the trail left by the Anubis' pod and head to Eros, where they meet up with Miller.
Joe Miller is a private police officer on Ceres station. He is asked by his boss to do a quiet, off-the-books look around for the daughter of a high-placed rich guy. The guy's name is Jules Mao, and the girl's name is Julie Mao. It appears as though Miller was set up to fail, for reasons we're not exactly sure about.
In Miller's investigation, he uncovers evidence of a whole bunch of connections between Julie Mao, Jules Mao, the Scopulii, the Canterberry, and by way of the Canterberry, the Donnager, and a ship called the Anubis. He also sorta becomes obsessed with Julie.
Miller's boss doesn't like that he's actually uncovering stuff, so she fires him. Now jobless, Miller sets out to finish his last case: finding Julie Mao. He uses his connections to Sematimba, one of the last actual cops left on Eros, to find out that a shuttle from the Anubis was docked at the station.
Not knowing if she was alive or dead, Miller uses the last of his money to buy passage to Eros. He tracks the person who "owns" the Anubis shuttle, Lyonell Polanski, to a hotel on Eros, where he meets up with Holden and the crew of the Roci.
Holden, Miller, and the rest find Julie Mao in her hotel room with all of the lights and monitors destroyed, but she's already dead. She appears to have died from the protomolocule. We find out from Dresden that it's a viable sample, and can be used to make the injections.
While Miller and Holden are trying to figure out how it all connects, Dresden and his people begin the operation.
It appears, at least to Fred Johnson, that someone was attempting to manipulate a war between Earth and Mars, and my belief is that it's the same people doing the protomolocule, in an attempt to keep people distracted from Eros.
As the Roci was flying away from Eros, Dresden sent a data stream to "Thoth" and Alex intercepted it.
I think this is everything....
Does this help?
