The family regroups after Mary's ordeal; Stan and Marshall search for a way to force Spanky to tell the truth about Chuck's drug trafficking; the FBI corners Mary.

To Monica's horror, Pete plans to be in an ultimate fight, and when he can't win but won't give up, she must decide her future with him. Chandler has a problem when his new boss is slaphappy. Phoebe sets Ross up on a date with a woman who used to be bald.

After a nightmare, Clark goes to the cave to confront his father Jor-El. Jor-El warns that the crystals have fallen into human hands and have triggered a new meteor shower which will annihilate the Earth unless he reunites the three crystals. Meanwhile, Lex helps Lana, who has apparently committed murder, but then turns against her to get possession of her Kryptonian stone. As disaster looms, Chloe and Lois try to find Lana while Clark attempts to reassemble the stones, and Jason returns to make things unpleasant for the Kents.

The team is investigating the ongoing murders by a signature killer. The killer has some knowledge of forensics and has left little evidence behind. With the investigation somewhat stalled, the sheriff invites the FBI to join the case. This makes Grissom angry and it only gets worse when Sara offers to bait the killer.

Chuck learns the most shocking secret of her life and refuses to forgive Ned. In order to take the Pie Maker's mind off of Chuck, Emerson gets him to solve the mystery of a man killing life insurance agents and hiding them in snow banks. Oscar Vibenius returns to investigate why Chuck has a unique smell. Meanwhile, the Aunts' antidepressant-laced pies begin to show some hallucinogenic effects.

In the third season finale, Allison's life, along with the lives of her family, is uprooted as her psychic abilities are revealed to the public. Allison must now find a way to catch the "recapitator" serial killer on her own, as she can no longer turn to Devalos or Scanlon for help.