The search leads to Coerthas, where the Ishgardians offer nothing in the way of assistance, distracted by their focus on the Dragonsong War, which has stretched every resource they have to its breaking point. Even as the adventurer arrives, the four high houses of Ishgard are set against each other by traitorous heretics loyal to the Dravanian Horde. What little assistance the Ishgardians don’t reject outright is thankfully enough to ingratiate the adventurer with House Haillenarte, who offers a formal introduction to Lord Haurchefant of House Fortemps, the only of the High Houses to welcome adventurers and sellswords from abroad. With Haurchefant’s help, the group is able to unravel a conspiracy against the weakened House Haillenarte, unmasking a holy inquisitor as a heretic of the Horde. Grateful, and humbled, the High Houses assist the group in locating Cid's airship, which was apprehended by the garrison of Stone Vigil just before the Calamity. Though the airship might still be there, the fort itself has fallen to the Dravanian Horde, and any attempt to reclaim it will require braving the scalekin within.
House Durendaire aims to retake the Stone Vigil from the Dravanians, but is unprepared to launch their assault. Instead, Alphinaud, Cid, and the adventurer cut a narrow path through the fortresses’ halls to the Enterprise's resting place–beside a sleeping ice dragon. As Cid and Alphinaud attempt to repair and launch the airship before the dragon can stir, Lahabrea appears. Correctly surmising that the group intends to slay Garuda, he warns of her power–far beyond that of Ifrit or Titan – and wakes the dragon, vanishing as it rises to attack them. The adventurer prevails against the dragon, and through the cold winds of the Vigil, the Ice Crystal of Light materializes. Though the Enterprise is in need of repairs, Cid manages to get it airworthy and the group make their escape. As the airship takes to the skies, Cid struggles to remember why this all feels so familiar, but his memories remain lost.
To bypass Garuda’s tempest, Cid harnesses the power of over-aspected ice crystals, hoping they will warp the wind-aspected aether of her storms into an element she can’t control. On the return flight to Coerthas, Cid thanks the adventurer for reuniting him with a part of himself he’d lost and struggles once more to retrieve his memories. Though he fails on his own, his efforts resonate with the Echo and, together, Cid and the adventurer organize the visions of his past–his childhood as a Garlean engineering prodigy, his time at Imperial court with Gaius van Baelsar, his defection to Eorzea and the rise of the Ironworks. If the adventurer is a Warrior of Light returned from Cartenau, Cid also remembers their final flight together to Rivenroad to slay Nael van Darnus. With renewed resolve, Cid reclaims his purpose of aiding Eorzea and flies into Garuda’s tempest.
In Garuda’s sanctuary, the Howling Eye, the Ixal have already summoned the Lady of the Vortex. Nearby, several of the beastmen guard a collection of Amalj’aa and Kobold prisoners, an ominously out-of-place sight in the Coerthan highlands. Despite her ferocity, Garuda is unable to overcome the adventurer, empowered by the Echo and five Crystals of Light. The zeal of the Ixal is not so easily extinguished, and even as she falters they endow her with crystals and worship. Enraged, Garuda resorts to attempting to temper the adventurer, but not only does the process fail on account of the Echo, but the power somehow responds in kind, tearing the aether bestowed on Garuda from her breast and coalescing it into the Wind Crystal of Light.
As the adventurer claims it, Gaius van Baelsar steps out from a concealed location nearby and mocks the primal, goading her into further defiance. Summoning the wind, she shears her Amaj’aa and Kobold prisoners asunder as they frantically pray for aid, their aether is torn from them and gives rise to both Ifrit and Titan. Alphinaud panics, calling for the group to flee. From the retreating Enterpise, they watch in awe as Imperial juggernauts deliver an enormous magitek beast that makes short work of all three primals, not only overpowering them, but seemingly absorbing their essences. Lahabrea watches on, assuring Gaius that this recovered Allag relic will only grow stronger with each primal it consumes.
Cid, Alphinaud, and the adventurer return to the Waking Sands, confident that the remaining beast tribes won’t risk summoning their primals while the Empire’s new machina exists. There, they meet Yda and Y'shtola, who it turns out were not present when the Garleans attacked. While the others contended with Garuda, Y’shtola and Yda were able to discover the others’ location, confined by the Empire at Castrum Centri in Mor Dhona. As the group rests in preparation to gather intelligence on the Castrum, Hydaelyn imparts a vision on the adventurer, affirming that the gathered Crystals of Light will protect them in the coming battle against the bearer of the Avatar of Shadow, Lahabrea.
The Ishgardians at the Observatorium confirm seeing the prisoners’ arrival in Mor Dhona from Coerthas. They also claim to have seen one of the airships make an emergency landing in Coerthas, where two prisoners matching the descriptions of Biggs and Wedge escaped. The group manages to track them down and save them from Imperial pursuers, and the group returns to Mor Dhona to plan their infiltration of Castrum Centri. To accomplish this, imperial uniforms and even a Magitek Reaper are stolen from local units, though the machina is damaged in its capture. To compensate, Wedge – nicknaming the magitek Maggie – installs a mammet heart to replace the magitek core. Its newfound sentience allows it to regulate the damaged parts, though it comes with some behavioral quirks.
The group succeeds in infiltrating the castrum and locating their comrades, but the escape goes awry and they are surrounded by imperial troops. Seeing this, the magitek reaper takes action despite having no pilot, confusing the soldiers and allowing Cid time to descend with the Enterprise and extract the Scions–though Maggie is left behind. From the air, the group sees Gaius consorting with Lahabrea near the now-completed magitek giant–the Ultima Weapon. Knowing the Scions bear witness, Lahabrea lowers his hood and removes his mask to reveal his hyruan vessel–Thancred. The victory feels hollow as the group make their retreat, Alphinaud curses himself for not having seen it sooner that Thancred had been possessed.
Fearing that the Eorzean Alliance leaders, believing the Scions dead, will surrender rather than face destruction by the Ultima Weapon, Alphinaud suggests that the reunited group appear before the nations’ leaders and declare their will to fight. Indeed, Gaius van Baelsar has offered Eorzea the same ultimatum he made long ago: surrender to Imperial rule and take up arms against the beast tribes, or be destroyed alongside them. Faced with an impossible choice between surrendering after all they’ve lost in resistance and asking the realm to risk what little it has left, the leaders of the Grand Companies consider conciliation. The Scions arrive in the midst of their meeting, where Alphinaud and Minfilia plead them to not give in to the foolish hope that Imperial rule would beget aught but further despair. Ashamed, the Alliance leaders consider why they took up arms in the first place, finding their resolve in the Scions return and vowing to fight.
Together with Alphinaud, the Alliance leaders outline an unprecedented operation, the largest counteroffensive in the realm’s history and the last thing the Garleans will expect. United, the Alliance will strike every castrum on Eorzean soil at once, culminating in an assault on the Garlean invasion force’s seat of power in Thanalan, the Praetorium, where the Ultima Weapon is housed. Noticing that at least twelve major factions will be fighting for the salvation of Eorzea, Alphinaud dubs the assault Operation Archon.
Signaling the launch of the assault, the adventurer leads a unit that intercepts Praefectus Rhitatyn sas Arvina at an inspection of Cape Westwind and slays him, leaving the western front without leadership. In the resulting confusion, the Maelstrom lays siege to Castrum Occidens while the Lominsan Armada blockades Castrum Marinum and, in the Black Shroud, the Twin Adders and sylphs surround Castrum Oriens. With Castrium Meridianum's supply lines cut off, the Immortal Flames attack, drawing its cohort into Northern Thanalan in defense. Returned from Cape Westwind, the adventurer’s unit, supported by Cid, steals into the now-vulnerable castrum interior and disables its defenses of the Praetorium within. Livia sas Junius mounts a defense within, but is slain in the adventurer’s charge. As the castrum’s defenses crumble, the Immortal Flames enter the stronghold and overwhelm the garrison while a second unit from the Twin Adder descends sabotage the railway between Castrum Centri and Castrum Meridianum before reinforcements can arrive.
With the Praetorium surrounded by Raubahn's forces, the adventurer boards the Enterprise and enters via an upper level airship dock. Gaius van Baelsar awaits in the command chamber, offering both Cid and the adventurer a place at his side, claiming that only as allies can they be permitted to live. Denied, the Black Wolf descends to the depths of the fortress towards the Ultima Weapon, sealing the cermet doors behind him. Cid remains in the command chamber to guide the adventurer as they give chase, recommending that they acquire magitek armor to break through the cermet barriers. By some strange coincidence, Maggie awaits in the armory, having been shipped from Castrum Centri and repaired. Armed with the Reaper, the adventurer makes short work of the barriers between them and the fleeing Legatus, but fall short just of their goal when the strain on Maggie’s hardware finally causes her to collapse.
Following his old friend’s voice from the command chamber, Nero intercepts the adventurer. Blaming Garlond for always being left in his shadow, Nero attempts to stall them in order to give Baelsar time to activate Ultima, but flees when he and his magitek are overwhelmed. Gaius is reached just as an elevator begins its descent towards Ultima. He berates the adventurer’s resistance, claiming Eorzea to be naught but delusion upon deception–false faiths, weak leaders, and destined to fall without Imperial rule. Seeing his words are wasted, he attacks, but quickly retreats towards the Ultima Weapon when he sees the adventurer’s true strength.
Controlling Ultima manually, Gaius engages once more. The adventurer is powerless, at first, but Hydaelyn soon intervenes, tearing the primals’ essences from the magitek and reducing its power, leaving it vulnerable to the adventurer, empowered by the Crystals of Light. Lahabrea appears as Ultima falters, confessing that within the weapon lies a weapon – the Heart of Sabik – stirred by the captured primals. Utilizing its power, he casts a spell of unrivaled power, Ultima. The Praetorium is leveled in an instant, leaving only warped metal and flames, but the battlefield on which Gaius and the party stand is untouched, shielded by Hydaelyn’s waning power. Unable to protect them a second time, Hydaelyn bids they attack, and the weapon is destroyed.
Frustrated, Lahabrea attacks personally, claiming that Hydaelyn is the source of a corruption that threatens all of existence and naught but the return of the one true god will save it. He underestimates Hydaelyn’s remaining power, however, and is exorcized from Thancred as Her light shines through the Crystals of Light. She assures the adventurer that the Darkness has retreated, but will soon return, beseeching them to be the beacon of Light for Eorzea and the realms beyond. As the Praetorium falls, Maggie appears before the adventurer and the unconscious Thancred, somehow restored, and bears them away from the collapsing wreckage. Left behind, Gaius stumbles to his feet, reflecting on his conquest ending in smoke and ashes as the flames consume him.
This concludes the Main Scenario Quests of A Realm Reborn patch 2.0, read on here.