The Mysterious Toppings Chest in Cookie Run Kingdom is crucial because it is a Resonant Toppings Chest. This means that you can choose Resonant Toppings of your choice for specific cookies to give them better stats.
Mysterious Toppings | Cookie Run Kingdom
Because these toppings are so sturdy, knowing exactly how to obtain Mysterious Toppings (and how to use them) is essential to making sturdy cookies.
Here are the Mysterious Toppings crates in CRK, unpacked and explained.
You can get Mysterious Toppings in Cookie Run Kingdom through time-limited events. You get chests from event quests or as rewards for logging in during events. This is how I got my first Mysterious Toppings chest. Once you have your Mysterious Toppings chest, you can use it to get Resonant Toppings.