Tim (Kieran Culkin) and Francis (Emile Hirsch) are best friends, doing their best to cause trouble without getting caught. Under the watchful eye of Sister Assumpta (Jodie Foster), the boys plot to unleash the ultimate prank, involving a man-eating cougar, their school's statue and a lot of cough medicine. While the boys imagine their exploits in a comic book called The Atomic Trinity, Francis begins his growth to adulthood with Catholic schoolgirl Margie Flynn (Jena Malone). Growing up is never easy, but it's never boring either.