Apoptosis is a process in which a cell self-destructs through the release of enzymes. In the Star Fox series, apoptosis is caused by an organism carrying cells which are purposed for self-destruction.
The Aparoids have a weakness, since their bodies contain many of these cells, thereby allowing a weapon known as the Self-Destruct program to obliterate all Aparoids in a single blow. But in order for the cells to activate the self-destruct program has to be fired into the Aparoid Queen who has to be severely weakened. The program is transported by Fox McCloud who manages to invade the Queen's nest and deploy it after destroying her armor, despite being able to flee and suppress the program, the Queen was eventually crippled and could no longer keep the program from activating. This destroyed all the Aparoids in the universe and released every being corrupted by them free from the Queen's grasp.