Apoptosis is an explotiable genetic weakness. The condition comes from cells that are created for the sole purpose of self-destruction. Most notably, the collective parasitic mind known as the Aparoid had Apoptosis cells within the Aparoid Queen. The Cornerians were able to develop a program to activate these cells and Team Star Fox was able to deliver the program into the Queen, thus destroying the Aparoids.
After the retrieval of the second Core Memory, Beltino Toad learned that Aparoids were susceptible to Apoptosis. Immediately on the Beltino Orbital Gate, he and a group of scientists created a program to activate the cells within the Queen while Team Star Fox and the remnants of the Cornerian Defense Force repelled a large-scale Aparoid attack on the Zypher Ring. Upon the total repelling of the assault, Beltino and the scientists finished the program and uploaded it into a delivery device. Fox stored this within his Arwing and the assault on the Aparoid Homeworld commenced.
Star Fox, at the end of the battle thanks to a heroic move by Peppy Hare, was able to gain access to the Aparoid Homeworld core. Both they and Star Wolf battled through the tunnels to the Aparoid Queen. After a quick battle, Fox opened a hole within the Queen which allowed enough room for the program to be inserted. He launched it into the Queen, but instead of immediately being destroyed, she supressed the program and made an attempt to escape. Slippy mentioned that if she were to escape, she'd be able to develop an antibody to it, so immediately the team gave chase. They weakened the Queen enough to where she could no longer supress the program, and the Apoptosis cells were activated. The Aparoid mind slowly began to destroy itself shortly thereafter.