Caution: spoilers ahead for The Expanse season 6 finale
What kills Marco Inaros in The Expanse's series finale, and how did the Rocinante crew harness such a powerful force against him? Debuting in The Expanse season 4, Marco Inaros began his journey as a Belter extremist causing trouble in response to the OPA's truce with Earth and Mars. Keon Alexander's character very quickly rose to main antagonist status, and has held that honor for the best part of 2 seasons. Marco built the Free Navy upon a philosophy of Belt domination, brought Earth to the brink of destruction, and helped disgruntled Martians betray their planet - all on his road to seizing control of the Sol system and its colonies beyond the Ring Gate.
The Expanse season 6's finale marks the final battle between Marco's Free Navy and the Consolidated Fleet comprising ships from Earth's UNN, Mars' MCRN, and Camina Drummer's Belter faction. Naturally, the Rocinante is along for the ride also. Marco's goal in The Expanse's final episode is to reach the Ring Gate's Medina Station, where he can hunker down indefinitely and control the various colonies beyond. The Consolidated Fleet must defeat him before he gets there, but an initial assault is scuppered when Marco misdirects his enemies by cunningly disguising his ship, the Pella.
Outfoxing the Inners once again, Marco Inaros has a free run toward Medina Station - and toward victory. Only a single ship stands in his way. Unfortunately for Marco, that ship is the Rocinante. Naomi Nagata and the rest of James Holden's crew devise a plan that'll destroy the Free Navy permanently as soon as the Pella's bow tickles the Ring Gate. Everything goes according to plan as Marco, the Pella, the Free Navy, and all (well, most) of the Sol system's problems vanish in a cloud of darkness.
The Expanse finale's Marco death is the same phenomenon Sauveterre's Barkeith suffered at the end of season 5, but where that was a random event, the Pella's disappearance is triggered deliberately. Way back in The Expanse season 3, Holden learned how the ancient alien species responsible for creating the Protomolecule was wiped out by an even more formidable power, and every time the Roci's captain passes through a Ring Gate, he senses these entities growing angrier. The mysterious denizens have been expressing their anger by making a small number of ships vanish while passing through the Ring's network.
As Elvi Okoye deduced earlier in The Expanse season 6, these attacks are not random. Her studies found a mass energy threshold - a tipping point between safe passage and total annihilation. One or two small ships will travel without incident, but push more energy through, and the bad guys appear. Naomi Nagata noticed that when the Rocinante seized control of Medina Station by launching dozens of cargo pods toward the surface, Ring entity ripples were already beginning to appear. This realization inspires her plan to win without engaging Marco directly. As the Pella draws close, the Rocinante bundles everything it possibly can through Sol's Ring Gate - missiles, bullets, and the exploding remains of the Giambattista. The energy created meets the required levels to annoy the Ring entities, and by the time Marco Inaros realizes what's happening, his ship is already committed to the transit.
Exactly what happens to ships and crews who fall victim to a Ring entity attack remains ambiguous in The Expanse's finale. Based on Okoye's Barkeith studies and the way the dark alien tendrils take chunks out of Marco Inaros' body like a water hose hitting a sandcastle, it seems the Dark Gods can completely obliterate all matter into energy as it passes through the Ring - organic and non-organic alike. Marco Inaros hasn't been transported somewhere, or taken prisoner. There is no Marco Inaros in The Expanse anymore.
The Free Navy's leader may be dead and its fleet decimated, but Marco Inaros' supporters are still peppered throughout the system. During the Earth-Mars-Belt conference immediately following Marco's death scene, The Expanse series finale confirms Free Navy remnants still exist. Nevertheless, the organization itself has collapsed without its charismatic chief. Drummer is the captain now, and her position leading the Transport Union should guarantee the oppression and isolation that pushed Belters to Marco Inaros' cause is a thing of the past.