In a shaft of light, Hitomi and the prince Van tranports to the world of Gaea, where Earth is known only as the "Mystic Moon" in the nightly expanse. Van returns to the capital of his country Fanelia to be coronated after obtaining the Energist crystal from the dragon. During the coronation rite, the Zaibach empire launches an invasion with Guymelef Alseides mecha, and Van must retrieve at his mentor Balgus's bidding Escaflowne, the legendary god of protection of Fanelia.

Once again, Hitomi sees a disturbing vision, this time of Allen's fort engulfed in flames. Van reunites with his attendant catgirl Merle after she escaped Fanelia's fiery destruction, but both she and Hitomi fall ill. Both eventually recover, but then Hitomi's vision of a Zaibach invasion comes true at the hands of a devilish youthful commander named Dilandau...

After his capture by Dilandau and the Dragon Slayers, Van is imprisoned aboard the Zaibach floating fortress Vione. Here, the Zaibach strategist Folken reveals his identity to Van and attempts to invite him into the folds of the empire. Fortunately, Hitomi uses her dowsing abilities to discover the Vione, and the crew of Allen's ship Crusade mount a rescue operation...

After the successful rescue, Hitomi and Van's party seek refuge in Paras, Allen's home and the capital of Asturia. However, the Zaibach forces and their entreaties to King Aston upstage their entrance. (Zaibach and Asturia have a non-aggression pact.) Folken meets with Van to offer a personal entreaty to join the Zaibach cause. Meanwhile, Dilandau attempts to avenge the grevious facial scar Van inflicted...

After a gladiatorial fight to ascertain the legendary power of the Ispano-built Guymelef Escaflowne, King Aston invite omi and Van's party into the royal palace. The king is about to marry off his third daughter Millerna to a noble merchant's son, but Hitomi is shocked by the not-so-discrete kiss between Millerna and Allen. Meanwhile, agents hoping to lure Escaflowne out into the open seize the opportunity to capture Hitomi...

Hitomi, Van, and his attendant Merle are forced to depart from Paras in the wake of the devastation Dilandau caused. Allen is imprisoned for having abetted them, and Millerna learns that the Zaibach forces intend to invade Freid. As Millerna attempts to free Allen to warn Freid, Hitomi's party tries to disrupt the operations of a Zaibach Energist quarry. The ensuing events forces one of them to reveal a closely guarded secret ....

A feather from Van invoke visions of the past for Hitomi, who sees the courtship of Van's parents and his early childhood. The Dragon Slayers pursue and confront the Escaflowne, and Allen appears as if by Hitomi's prayers to assist. Unfortunately, Allen sacrifices himself to protect Hitomi from a deflected liquid metal attack. Millerna appears in time to operate with her nascent medical skills on Allen's wounds...

After Millerna successfully nurses Allen's wounds, the party turns towards Freid, the kingdom where her deceased eldest sister Marlene married into the royal family. Here, they meet Marlene's son Prince Chid, a blue-eyed innocent who still remembers stories his mother recounted of the peerless knight Allen...

Suspicion of treachery falls on Hitomi and the rest of the party, and chameleon-like Zaibach operator Zongi (disguised as a Freid Praktu high priest) is sent to pry open her mind. During the ordeal, Hitomi reveals her origins from the Mystic Moon, but visions of Zongi's own past intervenes -- as well as a prophesy of death that send omi into a deathlike trance...

Hitomi's party exonerate themselves, and Duke Freid (the ruler of Freid who just returned) grants them an audience at his palace. With their input, Freid prepares for the imminent Zaibach invasion. Meanwhile, Millerna discovers a secret door in her sister Marlene's music box. It reveals a diary -- a diary recounting Millerna and Allen's past...

Zaibach devastates the capital of Freid, and the duke and Prince Chid flee with Hitomi's party to Fortona temple in the country's outskirts. The monks here present the duke with the sword that unseals the legend of the power of Atlantis. Folken directs the Zaibach troops towards the temple, intent on claiming the sword and fulfilling Hitomi's vision of a bloody outcome to the battle.

In the last battle, Van incurs life-threatening injuries which Hitomi discovers to match Escaflowne's battle damage exactly. Fortunately, Dryden (Millerna's betrothed) appears and uses his knowledge of ancient technologies to summon Escaflowne's original builders. The Ispano repair Escaflowne and in the process, heal the pilot whose blood pact intertwines his fate with the Escaflowne's. Thus restored, Van rushes to mete out vengeance upon the Dragon Slayers, despite the consequences.

Van is enveloped into the world of the dead, and Hitomi goes to retrieve him -- but not before envisioning the destruction of Atlantis. The previous battle's trauma disorients Dilandau as well, so Folken sends out Naria and Eriya (the intensely loyal leopard girl twins who directly answer to him) to continue the mission of capturing the Escaflowne.

Dryden discovers the location of the Mystic Valley (and purportedly also, the entrance to Atlantis) in Allen's father's diaries. In the process, Allen confronts his bitterment towards his absent father, and Hitomi discovers her grandmother also visited Gaea. The party is pursued by Folken's floating fortress until Hitomi's pendant and prayer opens a portal to Atlantis.

At the ruins of the legendary Atlantis, Hitomi, Van, and Allen encounter various figures in their past, including Hitomi's grandmother, Van's mother, Balgus, and Allen's sister and father. Hitomi also watches the history of Atlantis from the creation of the thought-realizing Atlantis Machine through the genesis of Gaea to Atlantis's eventual destruction.

After Van receives a new Energist from his mother, Hitomi, Allen, and Van tranports to Dornkirk's fortress when Dornkirk attempts to activate his Destiny-Altering Device. Dornkirk explains to the disbelieving trio his apparently well-intentioned motives for all of Zaibach's actions.

Three weeks have passed since Hitomi, Van, and Allen's ordeal in Dornkirk's fortress, and all of Asturia prepares for Millerna and Dryden's wedding and worries over King Aston's ailing state. Van give Hitomi an almost-but-not-quite love confession that disillusion Hitomi, making her vulnerable to Folken's test of the Destiny-Altering Device.

With her upcoming marriage to Dryden on her mind, Millerna ask omi for a tarot reading on its outcome. Hitomi reads a prediction of misfortune and disaster, but decides to tell Millerna a prediction of happy fortune instead. She hopes her thoughts and faith alone would be enough to change fate and reverse the prediction. Her hope is shattered by the entrance of fortune-enhanced soldiers Naria and Eriya at the wedding.

Hitomi surrenders herself before the twin Zaibach leopard girls, but the reemergence of the sun causes a debilitating reaction in the fortune-enhanced soldiers. Naria crashlands back on Asturia, and returns to the royal castle on foot to capture Hitomi again. However, the side-effects of the fortune-enhancement process continues to stymie she and Eriya and eventually leads to Folken rethink his cause.

Asturia's royal council discusses whether to submit to Zaibach or rally against the empire. Folken summons Van (and Hitomi) back to the ruins of Fanelia which he indirectly helped destroy. Here, the brothers and Hitomi face two dragons, and Folken reveals the truth about his disappearance during the pre-coronation dragon-slaying ritual ten years ago.

Asturia and its neighboring countries agree to unite their forces against Zaibach and prepare for war. Folken joins the allied effort against Zaibach and lends his expertise and knowledge, despite Van's doubt and lingering resentment. Also, Dilandau at last returns to strike preemptively on the assembled forces at Rampant Port and fight Van again.

When Hitomi asked to get away from this world of fighting, she found herself transported back to Earth. It is once again the day before Hitomi would make her fateful confession to Amano and thus encounter Van. Reliving the events would reunite her with Van, but at the risk of hurting her best friend Yukari and returning back to the war.