The Glowing Bottle is an item necessary for finding the Jade Pipe in the Dark Maze (on the 5th Floor of the house). The player is required to have it in their possession before even being allowed to enter the Dark Maze room at all.
You obtain the Glowing Bottle by combining several items:
- Petals from the Beautiful Flower in front of the Elder Tree after plucking her
- A Glass Bottle from the Poison Room, inside of the middle dresser in the top-right corner of the main room right as you walk in
- Water from the large underground river formed after completing the Skull Puzzle
Thus, it is not a singular puzzle needed to get this item, but rather a series of smaller puzzles. Though these puzzles are smaller, they are not necessarily less complex than the other, lengthier puzzles.
On your way back to the exit after obtaining the Jade Pipe, Viola will drop the bottle on the way back, breaking it.