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 ....

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...

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.

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.

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.

The pivotal battle between Zaibach and the allied forces continues. Even after the Basram army employs the "doomsday weapon" in the form of a devastating Energist bomb, the fighting goes unabated. Folken decides the only way to end the war is confront Dornkirk personally and end his vision of the Sphere of Absolute Fortune.