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Dan, despite its' initial apperance, is able to achieve insane manuverability, easily able to keep up with even E.S. Dinah in its' Mobile Interface form.
It first appears after Shion and Allen successfully steal E.S. Dinah from the Dammerung. In order to draw KOS-MOS out, Wilhelm sends Voyager in Dan, saying that in order to bring out the knight (KOS-MOS), they will need a villian to threaten Shion, and the "he" (Voyager) would fit the role best.
While on their way to Old Miltia, Dan, along with entire army of drones attack them. Allen is at awe at how the black E.S. can manuver so freely to above human capabilties. Just when the drones all aim at them, KOS-MOS arrives and completes the trasnformation of E.S. Dinah. With (what appears to be) an X-Buster, the drones are all destroyed, the black ES teleporting out of harm's way.
It does not make a reappearance until the very end of Xenosaga II, where The White Testament is introduced.
E.S. Dan first appears on the ruined planet of Michtam right after the battle against Richard on the E.S. Gad and Hermann on the E.S. Joseph. It takes their Vessels of Anima and flies into the city, Jin making a remark that it's taunting them to follow. It reappears to claim E.S. Issachar's after its' battle against the party, taking its' Vessel and once more departing into the city.
Once the party make their into the Cathedral, they are greeted by none other Voyager, who releases to them Canaan's true purpose and taunts Ziggy before battling them in the Dan. Afterwards, it is defeat, its' Vessel taken, and its' pilot follows not soon after.
It makes one final appearance during the final battle as part of Zarathrusta's limbs.