Phyrexia was originally created by a Planeswalker of unknown name and origin; all that was known about him is that he preferred to take the form of a dragon. And before you ask, no he was not Nicol Bolas. The plane was found by a Planeswalker called Dyfed after the death of its creator. She shared her discovery with the then-leader of the Thran Empire: a man named Yawgmoth.
This went as well as you might expect.
Shattering a powerstone and using their power to create a permanent portal between Dominaria and Phyrexia, Phyrexia was to be a paradise, a hospital for those infected by phthisis (a term borrowed from the real world; it means "consumption" and is a historical word for tuberculosis) and the world where Yawgmoth would rule as a god. His plan both did and did not work: he and his followers were locked away when Rebbec, one of the last Thran not under Yawgmoth's command, rejoined the soulstones that powered the portal and jailed the Ineffable in his plane.
"AFTER FIVE THOUSAND YEARS I'M FREE! IT'S TIME TO CONQUER DOMINARIA!" — The Ineffable, after the unsealing of Phyrexia.
Five millenia passed. Phyrexia, under the leadership of their new god, started to amass an army capable of invading entire planes. But their plans could not be brought to fruition because of the lock placed on Phyrexia. Until two brothers, Urza and Mishra, found the powerstone that Rebbec used to seal away Phyrexia. In a bout of tremendous stupidity they shattered the stone and freed Phyrexia. The Phyrexians agent Gix eventually corrupted Mishra forcing Urza to activate the Golgothan Sylex, which leveled an island, threw Dominaria into an Ice Age and formed the Shard of the Twelve Worlds, a fold in the Multiverse containing a dozen planes including Dominaria. Several Planeswalkers were locked inside the Shard, but there was no small amount of solace to Urza that Phyrexia was once again unable to access the Nexus of the Multiverse.
Until Freyalise, Jaya Ballard and Jodah (a descendant of the Brothers, it is unclear which one because Urza's wife slept with both him and his brother nine months before her son was born) removed the Shard with the World Spell (Freyalise using a combination of spells that would in-game generate infinite mana). This led to Urza trying to invade Phyrexia to destroy the plane and proceeded to conduct large amounts of ass rape. He failed and was rendered insane because of his attempt. During his insane period he encountered a defective Phyrexian sleeper agent named Xantcha and Ratepe (who looked exactly like Mishra), who helped him destroy other sleeper agents and eventually strike a blow at Phyrexia by destroying Gix, the right-hand man of Yawgmoth at the cost of Xantcha's and Ratepe's lives.
His madness cured by his time with Xantcha and Ratepe, Urza founded the Tolarian Academy which quickly became a target for the Phyrexians. Sending the sleeper agent Kerrick (or K'rrik) to destroy the enemies of Phyrexia, he managed to get a force of Negators inside the Academy. Only because of intervention at the hands of Karn his victory was undone when the golem traveled back in time and stopped him. But the victory was not without its cost: the island of Tolaria became wracked by temporal storms. K'rrik managed to use one to his advantage until Urza rolled in and roflstomped him for good.
As Phyrexia began to build an army capable of laying waste to Dominaria, Urza began to build his own. Starting the Legacy Project to create a race of humans capable of standing against the Phyrexians, it also the Metathran, tall blue-skinned pointy-eared humanoids. It's final product was the Legacy Weapon, a series of artifacts capable of standing up against the Ineffable and his forces.
Despite Urza's efforts, when the day finally came, most Dominarians were still painfully unready. The first wave of Phyrexia's invasion, a fairly conventional (for this universe) affair of biomechanical horrors flooding through planar portals, devastated entire continents. Millions more died from magically engineered plague viruses released into the wild. The defenders were not even united: the planeswalker Teferi refused to have anything to do with Urza's plans, and defended his homeland in Jamuraa with a massive spell that took it out of phase with the rest of the multiverse, which had nasty consequences for everyone involved later on. Nonetheless, the defenders rallied and won several significant victories, pushing back the Phyrexian forces and defeating Tsabo Tavoc, Yawgmoth's general.
This was all rendered completely irrelevant in the second phase of the invasion: the Rathi Overlay, where the artificial plane literally merged with Dominaria, bringing with it millions of Phyrexian soldiers and monsters and transforming parts of the plane into mini-Phyrexian ecologies. At this point, Urza led a group of planeswalkers - the Nine Titans - into Phyrexia itself in an attempt to destroy it from within. But deep within the plane, Urza was confused by the whispers of Yawgmoth and a questionable vision of his long-lost brother Mishra, and he defected to the side of Phyrexia, resulting in the deaths of most of the Nine Titans.
|Settings of Magic: The Gathering|
|Pre-revisionist:|| First Magic Sets - First Urza Block - Arabian Nights |
Legends - Homelands - Ice Age - Mirage
|Weatherlight Saga:|| Portal Starter Sets - Second Urza Block |
Tempest Block - Masques Block - Invasion Block
|Post-Weatherlight:||Otaria Block - Mirrodin - Kamigawa - Ravnica - Time Spiral|
|After the Mending:|| Lorwyn - Alara - Zendikar - New Phyrexia |
Innistrad - Return to Ravnica - Theros - Tarkir
|Two-Block Paradigm:||Kaladesh - Amonkhet - Ixalan|
|Never in a standard set:||Fiora (Where the Conspiracy sets take place)|