The Aeon Star first appears in New Super Mario Galaxy 2D. Bowser is looking for it as part of a plot against Mario, in which he would break the boundaries between the universes and set other series' villains against the plumber. Mario, Luigi, Princess Peach, the Toad Brigade, and Rosalina travel across the universe in an attempt to find it first, but are unsuccessful.
The Aeon Star finally turns up shortly after Mario reaches Bowser's Castle; Bowser takes hold of it and starts to carry out his plan. Mario defeats Bowser with the power of the Grand Stars, but the cosmic damage is done.
The Divine Council acts on the opportunity to crossover a large number of universes, causing panic and disarray across the realities. Meanwhile, the Splicers seize the Aeon Star as part of the top-secret Operation: Fusion. They fuse it with other fuel sources to form an unstable "Sun" in the Mainverse, using its energy for malignant purposes.
In Chapter 5 of Umbrella Waffle, the player travels to the center of the Sun with the thirteen Grand Stars of Super Mario Galaxy and Super Mario Galaxy 2. This further destabilizes the Sun and draws the Spicers' attention, starting the Multiversal War.
- According to Word of God, the Aeon Star was the biggest fuel source in the Sun, and the power of the Grand Stars destroyed it alone. This fact, combined with the Grand Stars reacting with the rest of the fuel, is the reason that the Sun destabilized so much.
- This also confirms that the Aeon Star was really destroyed.