The Queen's Domain Storm Gem sits on a large staircase in the Tower of Knowledge, and it gives the Holy Sword Endu its special attack meter. Picking it up unlocks the Raging Tempest achievement and pops on pickup, with no fight required.
On this page
Where the Queen's Domain Storm Gem is
Light Gargoyle III and Gargoyle VII with the Azure Torch on the numbered balcony, then take the passage those two open. Climb the big staircase toward Knowledge Keeper Wourha's study and the upper fast travel point, and the gem sits on that staircase next to the altar.
About a third of players hold the Raging Tempest achievement, so this is a mid-game pickup rather than a late one.
The Tower of Knowledge walkthrough has the balcony route.
What the Storm Gem does
The gem gives the Holy Sword Endu a special attack meter, the Raging Tempest. The meter fills as you kill enemies, and once it is full you fire the attack with R on keyboard by default, or Triangle/Y on controller. You do not need the sword in hand to fire it, and the game does not explain the mechanic well, so check your keybinds if you play on a controller.
The two large golden doors that stand on either side of the gem altar stay locked, and the gem does not open them.
The Holy Sword Endu guide covers the sword's specials.
Wind Gems are a different upgrade
There are five Wind Gems in the island and each one adds a single diamond to the Wind Dash meter, one more mid-air dash. The Storm Gem is not a dash upgrade. If a gap is still too wide after a dash, the answer is another Wind Gem, never the Storm Gem.
The sword jump guide shows how to spend the dashes.
Where to go after the Storm Gem
The stairs past the gem seem to dead-end, so jump off the big staircase below the gem and air dash onto the raised ledge underneath it, which is easy to miss from above. Pull the lever down there to rotate the staircase and open a new route, then find the dying soldier behind a cage near candles and a wall of flesh in the bookshelf room where you slot in books. He hands you the Forbidden Archives Key, and going back up opens the large golden doors that lead to the Necronomicon.