Xenosaga: Episode I - Der Wille zur Macht, the first chapter of a trilogy, is a Japanese-style sci-fi role-playing game, sharing many common themes and gameplay elements with Xenogears. The battle system is not unlike the one used in Xenogears (combo attacks, AP and EP gauges, etc. ), but random encounters are eliminated. Instead, the enemies are now visible and battles can be avoided. During combat the few upcoming ally and enemy turns are shown onscreen, allowing the player to make strategic decisions based on who will act next. A rolling slot moves with each turn as well, conferring a bonus such as added damage or bonus XP for any action on that turn. If the enemy would be in position to take an advantage then the player can expend a character's "boost" gauge to cut in and act next, although enemies can boost as well, and enemy boosts always over-ride player boosts. Each character has a unique tree of Ether spells they can learn by spending Ether points earned in battle, with lower spells requiring spells above them to be purchased first. After a spell is purchased, so long is it does not require a unique talent of that character, the spell can also be purchased and learned by any other character that can afford double its normal cost. The Anti-Gnosis Weapon Systems can be equipped with different weapons and accessories and can be used in combat provided that a character has enough AP on that turn to board their AGWS.

Shion is running final tests on KOS-MOS aboard the Woglinde when the crew retrieve a Zohar Emulator, one of thirteen replicas of the Zohar. Cherenkov monitors Shion's progress, but is also a U-TIC spy furthering their goal of finding the original Zohar. Following the Zohar Emulator's retrieval, the Woglinde is attacked by Gnosis. KOS-MOS self-activates and protects Shion's team, in the process killing Virgil with friendly fire to save Shion and Allen. KOS-MOS brings them and Cherenkov on board the Elsa, which is heading to their destination of Second Miltia. When a Gnosis attacks, chaos' ability to dispel them saves Cherenkov's life. The attack begins mutating Cherenkov, tormenting him with visions of his past as a soldier who failed to adjust to civilian life and killed many people including his wife. During these periods, Shion becomes concerned about KOS-MOS's behavior, and Allen worries about Shion's emotional state. Alongside these events, the cyborg Ziggy is dispatched to rescue the Realian MOMO from U-TIC, as data stored inside her could open the way to the original planet Miltia, lost in a disaster for which her creator Joachim Mizrahi is blamed. Ziggy rescues MOMO and narrowly escapes, fending off attacks by Margulis. Albedo, who is working with U-TIC for his own goals, sets out in pursuit of MOMO.