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Mysterious Presence is a side quest in Aniimo. Here's a walkthrough of Mysterious Presence and the 9 Voxel Cube locations, as well as how to unlock the quest, and its rewards.
To unlock the Mysterious Anomaly, you must interact with the glitch sign at the front of ChillBeanz Cafe in Astra.

The first Voxel Cube is received after encountering the strange anomaly during the beginning of the quest.

The second Voxel Cube is located southwest behind ChillBeanz after interacting with and repairing a glitched sign.

The third Voxel Cube is located near the Starwish Gacha building after interacting with and repairing a glitched sign.

The fourth Voxel Cube is located on top of the Super Claw building during the Mysterious Presence - Super Claw Malfunction side quest. Jump up the huge hologram at the top to make the cube spawn.
Super Claw Malfunction Walkthrough

The fifth Voxel Cube is located in the swing area on top of the Super Claw Building. To use the swing and spawn the Voxel Cube, bring out an Aniimo in the Lumin stage and circle around the swing three times.

The sixth Voxel Cube is located along a pathway east of ChillBeanz after stepping on numbered tiles on the ground in ascending order (1 to 8).

The seventh Voxel Cube is located by a seesaw west of Horizon Square after playing on the seesaw. Similar to the swing, you must use a Lumin stage Aniimo and press the Swing button as your character goes up.

The eighth Voxel Cube is located north of Horizon Square near a group of Aniimo playing music. Speak with Judy first, then tune the Chirpi, Tromber, and Cornet so that each one plays the same tone, which starts with Hey.

The last Voxel Cube is located on the overpass bridge heading northwest from the center of Horizon Square. It appears after stepping on a set of numbers written on the ground in ascending order (1 to 8).
Talk to Reno, the repairer to where you got transported. After talking to the repairer, go back to the Polaris Institute and ask Dr. Bohr regarding the anomaly.
Fast travel to the Boomblast Arena and go north towards the direction of ChillBeanz. You will see a glitch sign of Anii Apartment a bit to the southwest of ChillBeanz. You will need to solve the sliding puzzle, but don't worry as the there will be a picture of the correct image at the left of the screen as a guide for the puzzle. Solving the puzzle will make a Voxel Cube appear which you need to obtain.
Go to the Starwish Gacha where you will find the Challenge Glitch Sign. Solve the sliding puzzle like the previous glitch sign. Solving the puzzle will make another Voxel Cube appear which you need to obtain. Nova will call you and you need to return to the holo-lab in the Polaris Institute. Talk to Nova and you will unlock another quest, Mysterious Presence - Super Claw Malfunction.
Go back to Astra and do the Mysterious Presence - Super Claw Malfunction to get another Voxel Cube. Go to Super Claw and talk to Jiff. Go to the holo-projector at the top and then jump to make the cube spawn.
Go to the Swing area at the east of Chill Street and sit there. Play on it by pressing the Q button. You will need to fill the meter at the top of the screen to circle around. To do this, you need to time your press every time the swing swings to the back for max momentum to successfully fill the meter. Once you've circle around, a Voxel Cube will appear behind the Helmut in the same area.
Teleport to ChillBeanz cafe and then go outside to the right, then to the south and you will see numbers 1 to 8 on the ground. Step on them in order to make the Voxel Cube appear.
Go to the west of Horizon Square and play the seesaw with you Aniimo. Press the Q button every time your Aniimo is lowered to the ground and you are high up when playing to fill the meter above. Go to the thing that appeared behind the Hummin nearby after filling the meter to get the Voxel Cube.
Go to the North of Horizon Square where the Aniimos are playing music, and talk to Judy who is trying to remember a song she dreamt up. Offer to help Judy remember her memory.
Follow the last objective marker which will lead you to an overpass to the northwest of Horizon Square. You will see another set of numbers on the floor just like near ChillBeanz earlier. Step on the numbers in order to make the a block appear. Approach the block to get another Voxel Cube.|
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Thank you for pointing this out! We appreciate all the feedback and have now added all 9 Voxel Cube location on the page.
Mysterious Presence: All Voxel Cube Locations Walkthrough

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Thank you. The guide is incomplete or rather poorly explained.