From the Super Mario Wiki

The Omega-onion is an item featured in Mario & Luigi: Bowser's Inside Story + Bowser Jr.'s Journey. It is an ingredient required to make Skeletone Formula:D, along with the Giga-carrot and Ever Ice.

After obtaining a sample of the Giga-carrot, Bowser Jr., Kamek, Morton, and Iggy head for Cavi Cape in search of the Omega-onion. Shortly after Iggy goes missing and his Clown Car is found, Morton discovers that the onion is in the possession of an Oho Jee, who plans to eat it and get energy. Morton demands he give him the onion, but he refuses to, and after a long session of bickering, Kamek becomes involved, as well as Bowser Jr., who mistakes the Oho Jee for the onion.

They then decide to battle for the onion, and afterward, the Oho Jee reluctantly hands over the Omega-onion. He then leaves, allowing them to obtain the onion. Now having both the onion and carrot, they set out to get the Ever Ice, located at Bowser's Castle.

Later on, Broque Madame uses the Omega-onion, as well as the other collected ingredients, to make 200 servings of Skeletone Formula:D.