What does a Sparkling Cube do?

The practical effect is that every step of a normal capture stops mattering. No whittling the target down, no switching a party member into catch stance, no draining the Break gauge to stun it first. You throw and it lands. Alpha Aniimo still cannot be taken mid-fight, so a cube does not skip the boss fight itself, but it does remove the low catch rate you would otherwise face once the Alpha is down.

The second half is what you are really spending the cube on. Anything caught or hatched with one turns into its sparkling variation on the spot, which is the shiny version and comes with high stat rolls attached. Since the launch update that arrives at perfect potential rather than the epic grade you would usually be hoping for, so the creature you pull out is finished on arrival instead of being something you grind toward. During the beta the guarantee was a floor of elite instead, which is why older descriptions of the item undersell it.

Compare that against an Aniipod Ultra before you burn one. Ultras already guarantee a 100% capture rate, Alpha Aniimo included, so if all you want is the creature in your box the cube is wasted. Save them for species you actually want sparkling and perfect. Irisalis sits outside this entirely, since that bond is sealed with a crafted Legendary Aniipod in a one-time scripted encounter.

Using one on an egg

Cubes are not only a throwing item. During incubation you can select a Sparkling Cube from the right side of the interface, and it changes what the egg is going to produce: the hatched Aniimo comes out sparkling, with the same potential guarantee as a capture. Eggs out in the world only need a single interaction to collect, so the cube is the expensive part of that pipeline, not the egg.

One thing to watch. Dying during an Egg Heist run costs you your carried items, your backpack and your equipped gear. A cube sitting in your bag goes with them, so leave them stored until you are actually at an incubator.

Not settled: The potential guarantee moved at the launch update, from a floor of elite to a flat perfect, so which one you get depends on the build you are playing.