Urza continues to build a collection of artifacts that will defeat the Phyrexian invasion. After discovering the Thran mana rig in Shiv and beginning to rebuild the Tolarian Academy, Urza splits his time between the two projects.
With the assistance of his student Jhoira and Karn, the silver golem, Urza surveys the Thran mana rig in Shiv and uncovers its primary purpose: to create the rare Thran powerstones. They also discover that key parts of the facility were specifically designed for use by goblins. Urza and his party conclude that the hostilities between the viashino and the local goblins are territorial: the goblins' incursions into the rig are an effort to reclaim their "home."
To operate the rig at full capacity will require the rig's current residents (the viashino) and its previous ones (the goblins). Urza finds himself in the uncomfortable role of peacemaker as he attempts to convince both groups to work together under his guidance. Urza negotiates with the goblin chieftain and the viashino bey, and through barter, compromise, and force of personality, manages to unify all the area's residents behind his cause. The goblins and viashino agree to work together to produce the Thran metal framework of the Weatherlight and a functional, but uncharged, powerstone.
Meanwhile, Tolaria still suffers from the fallout of Urza's disastrous time-travel experiments, and many of the Academy's students and tutors are trapped in time rifts. Some, like Teferi, are frozen in "slow time" and appear to move hardly at all. Others in "fast time" have grown old and raised several generations of descendants. A Phyrexian sleeper agent named Kerrick is caught in one of these bubbles of accelerated time. As quickly as their limited resources allow, he and his small squad of negators are evolving into creatures that can survive the crossing back to normal time.
With the manufactured portions of the Weatherlight underway and Barrin keeping Kerrick's forces in check, Urza journeys to the sentient forest of Yavimaya to enlist its aid. Yavimaya and many of its denizens remember Urza's role in decimating Argoth, however, and he's taken captive by the power of the forest and its emissary, Multani. Urza's consciousness merges with Yavimaya's, and he's forced to experience firsthand the destruction he visited on Argoth. This also enables the forest to see and feel what Urza experienced during his failed raid on Phyrexia. The communion lasts for several years, but Urza's projects in Shiv and Tolaria continue, guided by his closest aides.
Urza's link with Multani and Yavimaya is interrupted when Kerrick's horde finally breaks free. Urza rushes to his Academy's defense, inadvertently bringing Multani with him. Urza gathers all the Shivan and Tolarian forces he can muster and, with Multani's help, they destroy Kerrick and his minions. Urza's cause has been graphically demonstrated to Yavimaya: if the forest doesn't help him, all of Dominaria may face the horror of Phyrexia. Through Multani, Yavimaya gives Urza the Weatherseed, a large organic construct that will grow onto the existing metal framework to form the Weatherlight's hull. Multani will guide the Weatherseed's growth, and Yavimaya also provides the template for a new race of faeries to help tend the seed.
Urza then must charge his dormant powerstone. He knows of only one way to energize the stone: to convert an artificially created plane into energy and capture it inside the stone. Urza has learned that artificial planes are unstable and eventually succumb to entropy; once his powerstone is charged with such a collapsing plane, it will function like an inexhaustible battery. Urza therefore returns to the plane created by the planeswalker Serra, where the Phyrexian assault has accelerated the process of decay, compelling Serra to abandon the plane.
On returning, Urza finds Serra's realm darkened and bleak - it's collapsing faster than he had guessed. Those unwilling to leave their once-perfect world when Serra left are led by Radiant, a proud and cruel archangel. Radiant remembers that Urza led the Phyrexians to Serra's realm in the first place and is openly hostile to the planeswalker. Despite Urza's earnest contention that all who remain will be killed by the plane's collapse, the ruling angels refuse to give up the control they've wielded since Serra's departure, even going so far as to slaughter those who would dare leave with him. After fighting a pitched battle and rescuing as many of the willing refugees as he can, Urza has little choice but to fold the planar energy of the rapidly collapsing realm into his powerstone - with Radiant and a handful of her militant angels still inside.
Back in Tolaria the mood is celebratory but guarded. The Weatherlight is ready to sail, the Legacy is nearly complete, and resistance to a Phyrexian invasion has begun to coalesce. Urza's gift for clockwork and artifice has rarely included an understanding of people, however, and the next stage of his plan is to find the Legacy's human component. He knows he must master this unfamiliar territory or all his efforts to prepare Dominaria for the Phyrexian invasion will be wasted.