With Yawgmoth destroyed, Phyrexia had no recourse, no retreat plan. The armies of Phyrexia fell. Dominaria became littered with the hollow shells left behind by the Phyrexian apocalypse. Since its defeat, Phyrexia is no longer a place. But it is still a force in the Multiverse. Thanks to an innocuous quantity of strange black oil, Phyrexia lives—and grows.
The glistening oil from Phyrexia is both a contagion and a means of colonization, a viral substance engineered to spread Phyrexian corruption wherever it travels. Without knowing it, Karn carried a trace of the Phyrexian oil within him, inside the Phyrexian heartstone granted to him long ago by Urza. Karn left traces of the oil in his travels from plane to plane, including the artificial world, the world Karn himself created: Mirrodin.
The glistening oil planted a virus on Mirrodin that spread. Unknown to most Mirrans, Phyrexia rebuilt itself, using their world as its host substrate. The metal structures and metal-infused inhabitants of Mirrodin create a perfect breeding ground for the spread of Phyrexian corruption. As the nascent civilization of Phyrexia expands in secret, it struggles to evolve a unified purpose, and the danger for the plane of Mirrodin grows.
The rise of New Phyrexia began at Ish-Sah, the epicenter of the Mephidross. Many creatures native to the Mephidross were already Phyrexians, perhaps even during Memnarch's day. Farther afield, the nim and Moriok serve as a foothold for Phyrexian corruption.
The Razor Fields fell to the Phyrexians quickly, scattering the leonin prides and isolating the loxodon. The last major fortress of the Razor Fields that has yet to fall to Phyrexian integration is the Auriok community of Bladehold. The once-roving civil force known as the Accorders now serve as Bladehold's military, fighting off Phyrexian assaults as best they can.
During the onset of the invasion, Phyrexian engines began pumping untold quantities of glistening oil into the Quicksilver Sea, to propagate its infection. The oil sea can transmogrify flesh into metal and vice-versa with alarming alacrity. Any non-Phyrexian unfortunate enough to be tossed into its fluid finds itself quickly decomposed and reprocessed into raw material for compleation.
Phyrexia always adapts to its surroundings in whatever manner will allow it to thrive. In its original system, Phyrexia only had access to black mana, so it grew as a black-aligned, necromechanical force. Here on Mirrodin, Phyrexia has evolved along all five colors of mana. This new form has made Phyrexia both stronger and weaker. It has spread into five color-aligned wings, allowing it to diversify and adapt more than ever before - giving it unprecedented strength and resilience in the fight versus the Mirrans. But this change has also introduced schisms in Phyrexia's core. What was once a monolithic threat united under Yawgmoth is now five distinct subfactions. Each bloc is Phyrexian through and through, but each has organized around a slightly different philosophy.
Each of the five Phyrexian factions is led by its Praetor. Each Praetor is a cunning Phyrexian ruler that sets its faction's agenda and embodies its principles. Each Praetor has its own policy about how best to wage war against the Mirrans. Each has its own opinions about the potential success or uselessness of the other Phyrexian factions. And each Praetor has its own agenda regarding Karn, the silver golem whose fractured mind many hope will forge a victory for Phyrexia. For his part, Karn has been vacillating between polar opposite mental states, sometimes raging against his imprisonment in the Phyrexia-controlled core, sometimes embracing his throne (as it, indeed, has embraced him) and acting as the new Father of Machines. The Praetors offer him self-serving counsel, hoping to "Wormtongue" their way into his new regime and/or exploit his frequent losses of sense. But they all agree - whether by unity, experimentation, enslavement, industry, or predation, Phyrexia will ascend as the dominant power on Mirrodin, indulging no free species.
Deep inside the Furnace Layer of the Phyrexian core hides an unlikely collection of rebel outposts: a pocket of Mirran resistance. Resistance fighters keep hostile Phyrexians at bay while surface-raiders smuggle living holdouts to the camps. Some strangely tolerant Phyrexians have turned a blind eye to these refugee outposts, a welcome but likely temporary condition that has allowed these camps to exist so far.