On the 20th anniversary, the Foothill High School, class of '87 alumni unearth the time capsule they buried to discover the remains of one of their classmates inside. Booth and Bones investigate the past lives of his classmates in an effort to discover the truth.

When a volunteer fireman is murdered at an ice rink, Booth and Brennan begin the investigation, but Booth must excuse himself due to a conflict of interest. When details come to light, Booth becomes a suspect in the homicide.

Stephen Fry returns as Dr. Gordon Wyatt. Booth, still suffering some lingering effects from his brain surgery, has to get re-certified for FBI marksmanship, but is not the accurate shot he was before going under the knife. He and Brennan investigate the death of a little person who was a former wrestling star.

When a subway train is thrown off the track by 60,000 gallons of flood water, a partially skeletonized body emerges out of the overflow. While Dr. Sweets, a passenger on the derailed train, copes with post traumatic stress, the rest of the team and intern Daisy Wick get to work on identifying the victim as Martin Aragon, a professional ghost writer caught up in a deadly love triangle. Meanwhile, Brennan releases her second book to great success, but has to accommodate a nosy reporter, and Sweets' near-death experience leads him to make a drastic decision.

The corpse of a truck company employee is found in the middle of the woods. After the victim’s son is questioned, Booth and Brennan visit his karate class in search of a motive. Back at the lab, Hodgins is going overboard purchasing lab equipment. Then, Booth’s son Parker returns from England and Brennan is apprehensive about how he’ll react to his new baby sister.

The Jeffersonian team rushes to prevent a viral outbreak while investigating the murder of journalist Mia Garrett after her infected body is found at a biohazard facility. When the mutated virus that killed Mia infects Jeffersonian intern Arastoo Vaziri, their only chance of saving him is by solving the murder. Tension and passion build as the team races against the clock to find the killer - and the cure.

It’s Halloween time at The Jeffersonian as the team gets a surprise visit from Lt. Abbie Mills and Ichabod Crane, who have traveled from the spooky town of Sleepy Hollow to help on a murder case of a young woman whose body is found on top of a 18th century military general’s headless body. The new foursome must figure out how to work together to discover who the 200-year-old headless corpse is and how the two murders are linked. Meanwhile, Booth and Brennan come up with the ultimate Halloween pranks to play on each other.

The crossover continues on Sleepy Hollow S03E05 Dead Men Tell No Tales (II).

Booth and Brennan go under cover at an Old West-style shooting competition; Angela and Hodgins talk about the future; Cam and Sebastian grow closer.