The show opens with a shot of a woman hiding in a room, voices are head in the background calling for those on the ship to report to battle stations. She appears to be wearing a uniform emblazoned with the name "Julie" on the front and the ship's name–Scopuli–on the back. The ship goes quiet and after some time Julie begins banging on the walls calling for help. Eventually she is able to free herself and make her way into the rest of the ship. The ship is quiet and some blood is smeared across the walls. Julie makes her way to the engineering bay, inside she finds the reactor lined swarmed by glowing blue protomolecule.

We cut back to the dwarf planet Ceres, located in the belt. There is unrest in the streets, belters feel as though they are working too hard, in unsafe conditions, and for little benefit, all to provide resources to the "inners"–primarily Mars and Earth–and there is talk of revolt. Here we are introduced to Star Helix detective Josephus Miller who is tasked by his supervisor with looking into the disappearance of Julie Mao, the daughter of an extremely wealthy entrepreneur Jules-Pierre Mao. The story is that Julie had a rebellious streak and became disillusioned with her father and began advocating for the belt.

Now on the Ice Trawler Canterbury James Holden is brought in to the captain's quarters to be promoted to executive officer, he explains that he can't since he has an intimate relationship with the navigator, but after some discussion he begrudgingly accepts. The ship is then hailed with an S.O.S signal from the Scopuli, the crew is initially skeptical thinking it might be bait from pirates attempting to lure them into a trap. Holden is ordered to get rid of the signal pretending they never heard it. He is disturbed by this and instead decides to record the signal in the ships logs, forcing the crew to investigate or risk legal action.

Meanwhile on Earth Chrisjen Avasarala questions an O.P.A (Outer planet alliance) agent accused of transporting banned stealth technologies, it is unclear as to where the stealth technologies are coming from since the O.P.A isn't likely to have the funds to be able to acquire them.

A sub-crew of the Canterbury including Holden, Naomi, Alex, Amos, and Medic Shed are dispatched to investigate the Scopuli and find a hole blown in the side of the ship that Amos claims is a breaching charge. In the cockpit of the Scopuli the crew finds a transponder, simultaneously the Cant detects a ship which appears–seemingly through stealth–and fires missiles which pass the rescue vessel and destroy the Cant, killing all on board.

In an attempt to find out where the stealth technology came from, Avasarala lies to her friend and UN ambassador to Mars Franklin, claiming that she has proof that Mars worked with the O.P.A to get stealth technology into their hands. She then monitors Franklin and discovers Mars has nothing to do with the stealth technology.

The remaining crew of the Canterbury pick up another ship on their radar, this time with a Martian signature. Assuming the Mars were the only ones capable of the stealth technology used against the Cant earlier, the crew becomes nervous. In an attempt to buy leverage with the Martians, Holden sends out a transmission (in defiance of the rest of the crew) stating that the Scopuli was set as bait and claiming on a hunch that the transponder found aboard was Martian technology. The message of Martian oppression resonates throughout the belt, and soon Holden and the crew of the Cant become a rallying cry for the O.P.A.

Once aboard the MCRN Donnager the crew of the Cant are individually interrogated, but despite Holden's questioning the Captain of the Donnager remain adamant that Mars had nothing to do with the destruction of the Cant. Eventually, a warship appears on the Donnager's radar, once again appearing from stealth and a battle ensues. When it becomes clear that even the Donnager–a high-tech Martian gunship–is no match for this stealth ship, the Captain of the Donnager orders Holden and the remaining crew of the Cant to flee aboard the MCRN Tachi, under the condition that they testify that Mars had nothing to do with the destruction of the Cant. In the escape, the Cant's medic Shed along with the entire crew of the Donnager are killed.

In the fire fight the Donnager's communications network was destroyed meaning no outgoing message was sent to Mars command from the Donnager to verify the Tachi was given freely. Fearing retaliation from Mars the crew seeks refuge with Fred Johnson, an O.P.A leader in charge of Tycho station. Johnson was once a military leader on earth but was nicknamed "The Butcher of Anderson Station" after laying firing on a ship filled with workers and their families protesting unfair conditions in the belt.

Chasing down leads on Julie's disappearance, Miller finds a data cube purchased by Mao with information about a new bio weapon discovered by researchers on Phoebe. Julie and the crew of the Scopuli hatch a plan to intercept the transport ship–the Anubis–as it is delivering the protomolecule from Phoebe to Eros, in an attempt to steal this new weapon for the belt. The plan goes horribly awry as the Anubis turns out to be a military-grade gunship, not a simple transport vessel. The Anubis kill all aboard the Scopuli, save for Julie who is locked away in cell by the crew.

However, en route to Eros, the bio weapon aboard the Anubis creaks containment and reeks havoc on the crew, except for Julie, locked away in a cell. She manages to break free of her cell and discovers the protomolecule throughout the ship but in particular, surrounding the ship's reactor. Having piloted ships before Julie is able to board a shuttle on the Anubis, and escape to Eros.

On Tycho station the crew of the Donnager strike a deal with Fred Johnson. Johnson mentions that he sent the Scopuli and its crew on the mission to intercept the Anubis, but that when thing's when south a lone survivor–Lionel Polansky–sent a distress call with coordinates. He tasks the crew of the Tachi–renamed the Rocinante–with finding the Anubis. Upon finding the Anubis, and the protomolecule inside, the crew of the Rocinante nuke the vessel and head for Eros.

Meanwhile, Avasarala uses the death of her friend Franklin to gain access his data on Martian shipyards. She finds that no evidence of Marian involvement in the Stealth ships. Later that day UN Under Secretary Sadavir Errinwright claims to have searched through the data himself and found conclusive proof of Mars' involvement.

Having heard word back from a contact mentioning that a short range shuttle of the Anubis was docked in Eros, Miller travels there and tracks Lionel Polansky–Julie Mao's O.P.A code-name–to a small dingy hotel room, where the Rocinante's crew has already arrived. Finding her dead the group, now consisting of Holden, Alex, Naomi, Miller, and Amos, head into the streets of Eros but find an unsettling scene developing in the station. Ships have been barred from leaving and thugs hired as police patrol the streets, forcing the occupants to receive what they claim are anti-radiation injections. Sensing trouble the crew of the Rocinante decide to leave and make way for the shipyards, while Holden accompanies Miller, in distress from Julie's death, as he searches for answers.

Miller and Holden come upon belters being placed in rooms and being irradiated (an attempt to spread the protomolecule more quickly). Both Miller and Holden are caught in one such room, receiving a lethal dosage of radiation. Finding anti-radiation and anti-nausea drugs, they manage to make their way through the chaos an back to the Rocinante, just as the contagion on Eros is reaching a critical mass.

Having escaped with their lives the crew of the Rocinante begins to unravel the mystery of the protomolecule. They manage to open a locked vessel salvaged from the Anubis, finding a cache of protomolecule stored inside. Now knowing the devastation the protomolecule can bring about, the crew decides to store the sample in a remote patch of space. However as they discard with it, the crew find out that the protomolecule may be extra solar in origin.

On Earth Errinwright and the rest of the UN meet to discuss the growing tensions between Earth and Mars. During their talks a UN ship beings making a hard burn towards Phoebe station, in an attempt to beat the Martian ship–now containing Sgt. Draper–to it. The Martians taking this as a threat fire long range missiles which destroy the Earth held station before the UN ship could arrive. Avasarala–growing ever more suspicious of Errinwright–decides to play dumb and, for the time being, allow Errinwright to think he's fooled her. Errinwright asks her to put out a statement claiming Mars is responsible for the stealth technologies along with the destruction of the Cant. As a result she becomes the scapegoat for the anger of the belt, and barely survives an assassination attempt outside the UN. Deciding she needs further protection, Avasarala seeks the help of a former UN military intelligence agent Cotyar Ghazi.

Back with Fred Johnson, the crew of the Rocinante learns that Eros was an experiment, designed to test and monitor the spread of the protomolecule, and furthermore that the data being collected is being streamed to an abandoned communications relay owned by Protogen, an earth corporation. Fred Johnson agrees to rally a group of O.P.A to aid in the assault on the station, while the Rocinante supplies protection from a stealth ship which defends the outpost.

In retaliation to the destruction of the Earth based–and Protogen operated–Phoebe station, the UN decides to destroy the Martian moon Deimos. Refusing to follow this order Admiral Souther resigns in protest. He is later confronted by Avasarala who tells him he has been reassigned, and asks what he knows about Fred Johnson. Souther hesitates but tells Avasarala that when Fred Johnson attacked the group of protesters in the belt, he was never told that they had surrendered, and that UN command had allowed him to take the fall.

Having successfully landed on the Protogen communication station, Miller is met with an unsettling scene. Finding the station guards armed with only gel bullets the O.P.A take the station easily. Upon finding the lead scientist Dresden, Miller executes him, fearing he would talk his way out of facing consequences for his involvement on Eros. Holden is furious believing the scientist could have provided valuable information and insists Miller leave the Rocinante immediately.

After the fallout from Deimos, Draper and her marines are anxious to wage battle with Earth but instead are sent to Ganymede station to protect the supply lines.

Avasarala grows suspicious that someone is attempting to pit Earth and Mars against each other and in a move tantamount to treason, she reaches out to Fred Johnson asking for any evidence that might lead to a ceasefire. In turn he sends her the coordinates of the destroyed Stealth ship which had previously been guarding the Protogen communication center. Avasarala then makes the gambit of freezing all of Protogen's assets pending investigation.

Realizing that Eros still poses a threat, Miller and Johnson devise a plan to steal the colossal Mormon ship, the Nauvoo, and use it to use as a battering ram to push Eros towards the sun and incinerate all the protomolecule left on the surface. Miller and a few other volunteers arrive on the surface of Eros first to plant explosives at the docks on Eros to prevent anyone from landing there again. However, due to a malfunction with one bomb, Miller is trapped on Eros, forced to manually prevent the bomb from detonating. As the Nauvoo nears impact Miller finishes his goodbyes with the crew of the Rocinante, when out of nowhere Miller feels a sudden jolt as Eros moves itself out of the Nauvoo's path.

Eros begins to accelerate, changing its trajectory, and now heading toward Earth. Holden and the crew of the Rocinante burn hard to try to catch up with it, but despite this, Miller on Eros mentions that he feels no acceleration (foreshadowing of the protomolecule's ability to manipulate acceleration). As Eros careens towards Earth, Miller decides to venture deeper into the asteroid's center, as he does he is met with more and more signs of protomolecule. Blue glowing structures line the inside of the station, and as he descends further he can hear the sounds of disembodied whispers calling out. Eros is now accelerating so quickly that the Rocinante can't keep up, fearing that the rogue asteroid will crash into Earth–killing billions–Avasarala decides to relinquish control of the UN's missiles to Fred Johnson, the only person with a tracking lock on Eros.

At the center of Eros, Miller finds protomolecule in the form of Julie Mao, as he speaks with her it becomes clear she is unknowingly controlling Eros. She is afraid and attempting to go back to her home on Earth. Miller pleads with Julie to stop Eros but she says she can't. Knowing it will kill him, Miller convinces Julie to divert Eros into Venus instead.

Following the Eros incident, Fred Johnson and the O.P.A now find themselves with more military might than ever before, having access to a large number of Earth's long range missiles. Meanwhile, the crew of the Rocinante–now believing the protomolecule is to dangerous even to keep hidden–agree to destroy it, a task given to Naomi. But rather than destroy it, Naomi instead sends it to Fred Johnson.

On Ganymede station, Draper and the other Martians are on patrol when they see the sky light up with gunfire. A stealth ship appears overhead, destroying the Martian ship in orbit along with all communications antennae. The Martian Marines on the surface see Earth Marines charging towards them and towards the Earth-Mars border, in the distance Draper can see they are being given chase by a feint blueish figure. Before they can react the figure is upon the Martians, killing all but Draper.

Draper–the only witness to the events–is picked up by Martians who want to know what happened. Bobby recounts the story of the Earth Marines coming towards them but is coached into saying it was only Earth Marines which attacked her and nothing else.

On the surface of Ganymede we meet Prax a botanist turned refuge who is searching for his daughter who went missing during the attack. Prax meets up with Holden and Naomi who now know protomolecule was at play on Ganymede and who have tied it to Ganymede Physician Dr. Strickland. The group finds that Strickland led Prax's daughter away during the attack and decide to help Prax search for her, hoping to get more information about Strickland in the process.

Bobby Draper along with a Martian escort head to Earth to give her testimony to the UN. The Martian story is that Earth marines headed towards the line but that an overeager Martian marine fired the first shot. Draper plays along but grows uncomfortable as they try to pin the blame on one of her dead Marines. Draper begins to insist to her Mars contact that she saw a seventh being that was not wearing a vac-suite.

In a moment of what seems like regret UN undersecretary Errinwright tells Avasarala he believes Bobby did see another being on Ganymede, and that it is likely a part of Jules-Pierre Mao and Protogen's research. When Avasarala presses him on why he thinks this, Errinwright admits that it's because he's been working with Mao since the protomolecule was discovered on Phoebe.

Beginning to distrust her Martian comrades, Draper escapes the hotel where she's being held, and eventually is found by Avasarala who tells her she believes her story about the creature on Ganymede, claiming it was a test of the this creature as a weapon. After being found by the Martians, Draper fights her way to the UN embassy and is taken in by Avasarala.

The crew of the of the Rocinante along with Prax get wind that Dr. Strickland never left Ganymede, but instead has taken Prax's daughter Mei, along with other children who share her genetic disorder, into an underground facility for experimentation. The crew infiltrates the base, but missed Dr. Strickland departing. After interrogating his associate, they learn Protogen is attempting to use the children as hosts to build a more controllable hybrid protomolecule capable of doing their bidding.

On invitation Draper, Cotyar, and Avasarala meet with Mao on his ship to discuss the protomolecule. Mao claims that the he is willing to work with Earth on the protomolecule and that they will discuss more aboard his ship. Once there Errinwright sends Mao a message stating a Martian military officer also interested in the protomolecule was dead and claiming responsibility for destroying a Martian ship bound for transport of a protomolecule sample. Errinwright is now the only person in power willing to work with Mao, and since Mao's assets are frozen, Errinwright holds all the cards.

As Holden and Naomi are alone aboard the Rocinante Naomi confesses to giving their sample of the protomolecule to Fred Johnson.

Fighting breaks out aboard Mao's ship. Draper and Cotyar manage to fight off Mao's small personal guard, while Avasarala creates a copy of the Errinwright's threat. Without Avasarala's voice of reason Errinwright is able to play the Secretary-General, getting him to declare war on Mrs. In addition, Errinwright convinces him that in fact it was Avasarala who had conspired with Mao on the protomolecule, and gets authorization to take her into custody on charges of treason.

Avasarala and Draper are able to escape Mao's ship in Julie's old racing ship, the Razorback. With the UN now in hot pursuit Draper burns hard to escape, leaving Cotyar back in Mao's ship. The two of them burn hard for a while but while Draper is trained for high G maneuvers, Avasarala is not and they have to slow down periodically. Fearing being caught by Errinwright's loyalists, they decide to send out an emergency distress call to ships in the area including the Rocinante, who reluctantly offer aid.

On Earth Reverend Anna arrives at the UN at the request of the Secretary-General. He claims she is an expert speech writer and wants her to help ease the growing unrest on Earth. She is reluctant, feeling the SG has not always done right by his title, but eventually agrees to help.

Without the voice of Avasarala, Errinwright further sinks his claws into UN Sectary-General, playing to the SG's ego and convincing him to launch preemptive strikes on Mars to end the war quickly and save the lives of Earthers.

Eventually the UN Agatha King–captained by Commander Souther–is able to capture Cotyar from Mao's ship. Despite being the commander of the ship Souther begins to grow suspicious of Admiral Nguyen, who rendezvoused with the Agatha King earlier. Nguyen repeats to him Errinwright's lie that Avasarala worked with Jules-Pierre Mao on the protomolecule, and begins to strategically place crew members throughout the ship who are loyal to him. Nguyen's men slowly squeeze Souther out of decision making and restrict his access to his own ship.

On Io Jules-Pierre Mao meets back with Dr. Strickland to check on the progress his research into creating protomolecule hybrids by infecting children with a rare genetic mutation. The progress is slow and while he is there, Mao meets Prax's daughter Mei. As they speak, Mao begins to connect with her and we can see the beginnings of regret forming.

Nguyen orders the Agatha King to make way for Io on a "top secret" assignment. With the help of those loyal to him, Commander Souther is able to get a speak briefly with Cotyar alone. Cotyar explains that he and Avasarala met with Mao and that Mao was going to testify against Errinwright in exchange for immunity and all the information Mao had on the protomolecule. He also tells Souther that while he has no proof, Avasarala has a recording of Errinwright's admission of guilt. The crew of the Rocinante then make for Io, learning that it may be where Dr. Strickland is holding Prax's daughter.

At the behest of Errinwright, Earth launches an all out assault on Martian military ships throughout the system. While they simultaneously destroy most of the vessels, one Martian warship is able to release a nuke before it is destroyed. The nuke strikes Earth, killing millions, Reverend Anna is distraught and confronts the SG, realizing he is only interested in serving his own vanity.

In a moment of clarity Mao confronts Strickland. He admits shame in what they are doing, claiming he wants no part in the torture of children and orders Strickland to shut the project down, but Strickland continues in secret.

The crew of the Rocinante, along with Draper and Avasarala arrive at wreckage of the MCRN Kitter Chennamma, one of the Martian ships destroyed during Earth's first strike. They find three Martian survivors, and agree to rendezvous them with another MCRN ship, if they promise to get their commanding officer to transmit Errinwright's confession to Admiral Souther. The message eventually makes it's way back to Earth and Errinwright is arrested.

A crew member loyal to Souther shows him the clip, realizing what this could mean about Admiral Nguyen–one of Errinwright's most loyal allies–Souther prepares to overthrow Nguyen. With the UN Agatha King nearing Io, a fight breaks out between those loyal to Nguyen and those loyal to Souther. As the fight draws to an end Nguyen shoots and kills Commander Souther, and retains control over the Agatha King.

As Strickland fears his work will be discovered by the UN, he orders the release of all hybrids via pods ejected from Io's surface. One such pod strike the Agatha King, the hybrid along with the protomolecule begin to spread throughout the ship.

The crew of the Rocinante–now on Io–fight through guards and Draper fights and kills a hybrid to get to Strickland. The crew is able to find Prax's daughter Mei along with Strickland. Amos convinces Prax not to kill Strickland, saying "you're not that kind of guy", and instead kills him himself, and they arrest Mao.

Naomi and Alex board the Agatha King in an attempt to save any survivors, but it's too late. The protomolecule has spread throughout the ship and gotten into the ships reactor, causing it to over heat. They escape but both Nguyen and Cotyar are left inside when the ship explodes. As the crew meets back aboard the Rocinante, we see news coverage of protomolecule vessel rising up out of Venus.

Some time passes when we pick the story back up and Avasarala is sitting in the office of the Secretary-General briefing the citizens of Earth, Mars, and the Belt about the ring formed by the protomolecule vessel on Venus. When the ring is fully formed, one rock-hopping Belter decides to fly through it. As he passes through the ring at high speed his ship decelerates immediately, killing him in the process.

The crew of the Rocinante are now playing hosted to a two person film crew documenting their lives. The crew was hired by a wealthy benefactor who agreed to pay the crew's legal fees–imposed by Mars as a result of their ownership of the Rocinante–in exchange for their cooperation in the documentary.

Meanwhile, Naomi has joined Drummer aboard the O.P.A Behemoth–previously the Nauvoo–along with Ashford, a man who worked in the O.P.A under Anderson Dawes.

It soon becomes clear that the documentary crew is there to do more than just document. One of the film crew replaces a chip in the Rocinante with another that he carries.

We are now introduced to a nervous new technician Melba aboard a UN servicing vessel. She is seen attaching an explosive device to a service panel, and when caught appears to unleash extreme strength and kills the engineer who found her. She disposed of the body and transfers to the UN Thomas Prince, crossing paths with Reverend Anna.

Aboard the Rocinante Holden begins to have visions of Miller–who refers to himself as an investigator–he is able to correlate the origin of the visions to the Belter crossing through the ring. Miller speaks to him in cryptic sentences, he mentions that while on Eros he told a fellow O.P.A to 'watch the doors and corners, if you don't come in slow, the room will eat you alive.'

The service vessel Melba planted the device on blows up and a message is broadcast to all ships in the area. The message appears to be coming from the Rocinante and shows Holden declaring the ring as the O.P.A's property and claiming responsibility for the destruction of the service vessel. As the message plays we can see Melba smiling to herself.

In an attempt to distance themselves from Holden, Drummer and Ashford decide to fire on the Rocinante, attempting to prove that this message is not representative of the Belt's views. As missiles approach the Rocinante, there appears to be no escape. Miller once again appears to Holden repeating once more 'if you come in too fast, the room eats you…' Holden and the crew bank on Millers advice and enter make for the ring, slowing down just before passing through.

During flashbacks we learn that Melba is really Clarissa Mao, a second daughter of Jules-Pierre Mao, and furthermore that someone she once new in her former life is currently aboard the Thomas Prince.

Having received information that the Rocinante survived it's passage through the ring and wanting to have one of their ships inside, the Belt's Behemoth, and the UN's Thomas Prince enter the ring. As the ships enter, it appears that the ring has a sort of speed limit, applying to all things traveling within it.

Upon entering they find that at the center of the ring there is a planet-like mass of protomolecule, which Miller calls "The Nucleus". Miller reaches back out to Holden telling him that it's important he go down to the nucleus is he wants to learn the truth. Driven by his desire to understand what's happening, Holden sets off towards the nucleus in a vac-suite.

When the Martian vessel realizes Holden is heading for the nucleus, they dispatch four Marines to meet him, among them is Bobby Draper. As Holden nears the center of the nucleus, Miller mentions that he has vast knowledge of the ring system but that he needs Holden since he has a physical form. The vision alludes to being able to manipulate Holden's neurons in ways which cause him to visualize Miller, down to the voice, clothes and hat.

Miller asks Holden to connect the gap between two synapses at the center of the nucleus. Before he can, the Martian Marines arrive, Draper attempts to talk Holden out of it but before she can Miller reaches out, in reaction several of the Marines fire weapons, and one trows a grenade which destroys a portion of the nucleus. As soon as this happens throughout the ring all ships are immediate slowed down. The massive deceleration kills hundreds, and damages many of the ships.

Holden connects the two synapses and sees the events of the show playing in reverse. The vision ends with wholes appearing in all around the surface of the ring and a beam of blue light being shot from the nucleus, through one such hole and at what appear to be the sun. The sun turns blue and explodes while Holden screams in horror.

As the ships in the area reel from the destruction caused by the ring, Clarissa Mao sees an opportunity to board the Rocinante, in search of Holden. She hates him for her perception of the role he played in Julie's death and the arrest of her father. However she is detained and we learn she was hired the film crew and was responsible for the false message claiming the ring for the O.P.A appearing to be sent by Holden. Her attempt to kill Holden is thwarted and she is detained.

While Holden believes the ring is not trying to harm them, but rather is reacting to what it perceives as threats, Ashford disagrees. In the wake of the damage from the deceleration, Ashford begins to view the ring as a threat. He feels it should be destroyed, and mentions that it is still possible to see within the ring, meaning light must be unaffected by the speed limit of the ring. He devises a plan to divert the Behemoth's power to an onboard laser, using it to destroy the ring. Ashford is aware that destroying the ring may lead to the death of all those inside, but feels it's the only chance they had to save the rest of the system from the ring.

While being held aboard the Behemoth, Holden finally has another vision from the investigator. After the vision, Holden claims to know what needs to be done. He along with Drummer, Naomi, Amos, Alex and Anna make their way to the Behemoths communication relay. Anna sends out a message telling all ships in the area to shut down their power. While nothing happens right away the message propagates throughout the fleet and one by one the ships start to power down.

Ashford is unconvinced however and moves forward with his plan. He almost succeeds if not for Clarissa Mao intervening. The crew shutoff power to the behemoth–the last ship still powered–and as the power is turned back on, we see holes begin to appear all along the surface of the ring, just like in Holden's vision. In a final conversation with Miller, Holden expresses that he thinks Miller's goal the whole time was to open the ring gates, and that he doesn't believe the ring gates were opened to help humanity. The season closes with Holden saying to Miller, "When you connected me to the station I saw something… the civilization that build the rings is gone, wiped out, what could have killed them?" Miller responds "That's what I'd like to know… I'm gonna need a ride", and as Holden–along with the Rocinante–passes through the ring gate, a blueish light appears to enter him.