When fellow villager and kunoichi, Momiji, is kidnapped by the Black Spider Ninja Clan, he is forced to find her, while uncovering the secrets behind the mysterious Dark Dragonstones and their relation to the Dragon Lineage.

Although he does not have a multitude of weapons like before, he can still perform his signature Izuna Drop and absorb nearby essences, given off by slain enemies, to unleash powerful attacks, known as Ultimate Techniques.

After a training session with the up-and-coming kunoichi, Momiji, she is kidnapped by members of the Black Spider Ninja Clan, on orders from their leader, Obaba, who hopes to obtain the Eye of the Dragon for the ancient Fiend, Ishtaros.

As Ryu desperately searches for her, he is suddenly transported back to the monastery in Tairon, capital city of the Holy Vigoor Empire, where he faces hordes of Fiends in the vicinity.

Unfortunately, the will of the Dark Dragon embedded in the stones is too strong for the Fiends to handle, thus destroying the symbolic Emperor, before it can fully resurrect, and encases Ishtaros in a cocoon.

They return to the Hayabusa Village and after Momiji visits Kureha's grave, promising she will become stronger to better protect herself and the Eye of the Dragon, joins Ryu to continue her training.

[6] One of Itagaki's goals with Ninja Gaiden DS is to create a game that can be played by all gamers everywhere, saying that his other titles "have traditionally targeted men above the age 18 and Westerners."

An example of this is that the characters that are traced to perform ninpo magic, were originally kanji; this was changed to the more "culture-neutral" Sanskrit to make things fairer for non-Japanese audiences.

[9] Reviewers praised the good visuals and intuitive controls, but a common point of criticism was its short length, six to seven hours, and lack of the difficulty compared to previous games in the Ninja Gaiden series.

[13] GamePro said in its early review, "As a standalone DS game, Ninja Gaiden: Dragon Sword is an amazing adventure almost at the level of [The] Legend of Zelda: Phantom Hourglass.

"[27] GamesRadar+ gave it a similar score of four stars out of five in an early review, calling it "a short ride, but like any quality roller coaster, it'll rattle your senses and challenge your reflexes.