The game retains the original's focus around the concept of "Magnus" – magical cards that capture the "essence" of items found in the in-game world, where the concept is still used as a plot device, for in-game item management, and as a basis for the card-themed battle system, albeit with minor tweaks.

[1] Similar to the original, the player plays the role of a "guardian spirit" that can break the fourth wall to interact with the game party through dialogue options.

[2] Unlike typical role-playing games, the Baten Kaitos series uses a mechanism where all in-game items are stored in magical cards called "Magnus".

In addition to playing through the game's main narrative, many side quests exist as well, including on-going efforts to restore the abandoned village of Sedna.

[4] The game does not contain random battles; enemy characters are visible on the field, and the player is able to choose to fight or avoid them.

[3] The main race of characters are human-like in nature, but possess bird-like wings on their back that assists in flying in small short bursts.

The main character, Sagi, works for the Alfard Empire in an elite unit, the Dark Service, that reports directly to a powerful politician, Lord Baelheit.

They encounter a giant beast called an Umbra, which Guillo has been mysteriously programmed to defeat, and meet up with the third and final member of the party, a young woman named Milly.

The three of them work to clear Sagi's name while trying to uncover the nature of the threat causing unrest among Alfard's various power-hungry politicians.

The group encounters more Umbra on their journey, learning that they are "afterlings", pieces of an ancient, evil god named Malpercio.

They discover the visions are real scenes from the past, and that Malpercio was not a god, but simply a group of warriors who solicited the help of dark forces to defeat Wiseman.

The project, ordered by Baelheit on behalf of Olgan, was abandoned after a mishap, but Sagi still lived on with pieces of Malpercio within him.

Baelheit reveals that Milly is half-Machina; when she was just a child, a failed experiment similar to the "Malideither Project" tore her in half and killed her mother.

He completes Tarazed, a huge flying mechanized fortress, and orders everyone to move onto it, as he intends to destroy the continents.

Sagi and Milly return to Alfard, happily reunite with family and friends, and eventually decide to elope and move to Mira.

[14] The developer's aim was to create a similar experience to the original game, while streamlining, lessening, or removing aspects of it in the process.

[15] In 2003, Honne had pitched a sequel to the Mother/Earthbound, involving a claymation styled background, to Nintendo; while the project was rejected, the concept was revisited and implemented in a portion of Origins in the magical town of Sedna.

[18] While no official reason was given for the change, Nintendo proceeded to buy Monolith Soft from Namco shortly after the completion of the game.

[22] The game's release dates would make it one of the last major titles released for the GameCube, with many Nintendo published titles at the time, such as Super Paper Mario, The Legend of Zelda: Twilight Princess, and Fire Emblem: Radiant Dawn being pushed towards the then-upcoming launch and early lifespan of the Wii instead.

[24] The team did not feel restricted by sticking with the GameCube's then-aging technical hardware limitations; some content was cut, but this was strictly due to time and budget restraints.

Other new features include two new game plus options that allow the player to retain materials from a prior playthrough or set up new restrictions to make a second playthrough more difficult, the ability to skip cutscenes, an auto-saving feature, and the ability to speed up both battles or general gameplay by up to 3 times the original speed.

[38] GameSpot and GameZone largely echoed their sentiments - praising the level of content and sidequest and its ability to build off of the original Baten Kaitos, but felt that some could be scared away by the difficulties in battles and grinding involved to advance the game.

[7] The game's translation and localization was praised by many reviewers as well,[3][5] as was the improvement of quality in the voice acting, which was panned in the prior entry.

[40] In 2018, Honne revealed that a Baten Kaitos 3 had entered pre-production planning shortly after the conclusion of development on Origins/2, though his details differed greatly from the 3DS reports.