Per wiki policy, this page contains unmarked spoilers. You Have Been Warned!
Although Lighter and Softer when compared to the first iX game there are still some noteworthy creepy moments.
- Empty Vessel is a track that plays after Null "dies" to become one with the teleporter. It's downright haunting and ominous, not helped that Null's motionless and bloodied husk is now front-and-center for the menu screen for the remainder of the game (that can catch first time players off guard) until the game has been completed.
- The "Hanging Gardens 2" stage.
- The stage starts out normal like the first one, until you venture further and discover that the area is corrupted. What was once a tranquil and serene looking garden has been replaced with a creepy and surreal atmosphere; with a dark purple solid floor with purple lines and further ahead is dominated with cables on both the floor and ceiling, a near reddish sky, a glitching diamond at a distance, and is in a state of perpetual rain. It symbolizes Mother's detoriating sanity that affects even the very garden she resides in.
- The enemies for this stage are Angelic beings that revert back to their pod forms which has a startlingly menacing appearance that contrasts their heavenly and beautiful forms that they take, and the Aluraune enemies (who normally have a robotic face) eerily has Lola's likeness here (which she, for some reason, doesn't take note of it), which act as a foreshadowing to Mother's true identity.
- If you decide to harm Kohaku enough times before rescuing her (right after Mother is defeated). Mother has completely taken over Kohaku's body. The epilogue shot is of her having just cleaned the lab, causing both Copen and Lola be off-put by her sudden change of behavior. Then as the two leave, we are treated to a shot of "her" menacingly glancing at the side, now sporting glowing eyes, in a pitch black background only dimly lit with a purplish tint accompanied with a Scare Chord, and declares that she will be with Copen... Forever (for bonus horror, accessing the main menu right after obtaining this ending results in Kohaku saying "we'll be together forever, Copen"). Now imagine what happens to Lola, Jin, Maria, Kyota, and especially her older sister Blade when she is alone with any of them....
- Despite the energetic battle theme, during the fight with Mother's Idol Form, if she's at her last health bar, she'll activate her Limit Break. While she does so, we get a close-up of her skeletal face (accompanied with glowing red eyes that rains bloody tears) while casting that betrays her angelic appearance. It's a minor Jump Scare for those who least expect it.
- The twisted nature of a lot of the Gravekeepers from ages of solitude. They are Workers who have tried and utterly failed to revive the human race by constructing locations meant to jumpstart a new era, but it has been so long that they've either given up or turned ruthless. Even the Mother Computer has had it with her creator's final order to repopulate human life that she cannot disobey, and has Kohaku kidnapped not to extract new human DNA, but to take control of her so she may give herself an order to destroy everything in a suicidal rage.
- Ypsilon gets some horror points for existing as a false copy of the Creator that Mother yearns to see again. At one time, Mother found him too inadequate to fill his shoes and abruptly scrapped him and left his Worker template body to litter the wasteland like an abandoned corpse. However, when Copen comes into close proximity of it, Ypsilon's remains scan Copen and regenerate the Pix that make up his body, albeit damaged. Ypsilon is forced to relearn his existence from scratch until he manages to reunite with Mother and prove his continued worth, but his efforts to please her grow increasingly desperate, and overall reflect that he's rapidly going insane, and the only way to give Ypsilon release is to utterly destroy him.
- Mother turns out to be the equivalent of Lola in the alternate world, and even in the Good Ending, where her spirit joins the Creator in death, and the corruption in the Hanging Gardens turns to a beautiful flowered landscape, there is still the dead and smoldering pod Mother's consciousness embodied left behind, leaving an ugly burn on what should be a picturesque homegoing.
