Sweets (John Francis Daley, far left) was killed while working the conspiracy case with Booth (David Boreanaz, center) and Brennan (Emily Deschanel, far right) in the "Bones" Season 10 premiere. FOX

Bones” returned to Fox on Thursday for its 10th season premiere. Fans will remember that in the Season 9 finale Booth (David Boreanaz) was framed for the murder of three FBI agents (who were really Delta Force Rangers trying to kill him) after digging too much into the McNamara conspiracy. As a result, Booth started this season in prison.

And Booth is not having an easy time in prison. Locked up among many of the men he helped put away, Booth was in two prison fights before the opening credits even rolled.

Meanwhile, Brennan (Emily Deschanel) and her team at the Jefferson Institute had begun work examining the body of Harold Cooper -- who's been dead for 16 years. Cooper was an EPA official who was a central figure in the blackmail information Brennan and Booth found in the Season 9 finale.

Brennan visited Booth in prison and became worried after seeing wounds from one of his fights. She suggested they blackmail the prosecutor (J.D. Cullum) in the case with dirt they have on him from the conspiracy files. Booth forbade it, but Brennan (in one of the more entertaining scenes) did it anyway and Booth was released from prison just minutes into the episode (so much for that storyline).

At the lab, the Jeffersonian team discovered that Cooper did not die of cancer and was probably murdered. Furthermore, other injuries from years before, on record as a fall down the stairs, were suspicious and Brennan suspected a car accident as the real cause.

Back at the new house (Booth and Brennan’s old house was destroyed in the Season 9 shootout), Booth conducted some digging on Cooper and found out that he had denied the construction of a new chemical plant to a Sanderson chemical executive and turned up dead days later. Two weeks after this death, the plant was approved. Booth paid a visit to Hugo Sanderson (Sam Anderson), the company's CEO, for a little intimidation.

Booth sensed that someone was following him and discovered FBI Agent James Aubrey (John Boyd), who was under orders from Director Stark (Sterling Macer Jr. ) to keep Booth out of trouble. Booth demanded that Stark return his badge and gun and afterward Sweets (John Francis Daley) reminded Stark that he had no legal choice (with the charges dropped).

Booth went back to Sweets’ house, where he learned that Sweets and Daisy (Carla Gallo) had gotten together while he was in prison and that Daisy was pregnant with a baby boy. Booth was visibly touched. Sweets went to meet with Brennan where he explained that Booth was struggling, though, after losing trust in the people around him, i.e. the FBI..

Later, Booth and Brennan paid a visit to the ER doctor (David Fabrizio) who treated Cooper for the alleged fall wounds, but he denied knowing anything suspicious. Booth, though wasn’t buying it. He returned later and after shaking him down, he learned that the doctor had been blackmailed to cover up the car accident injuries.

Aubrey showed up at Booth and Brennan’s house at night and explained that Stark was part of the cover-up and told him to ignore a connection he found between Sanderson and the McNamara case. Could Aubrey win Booth's trust?

Back at the lab, an official showed up to take back Cooper’s remains, suspiciously claiming that a family member requested them. Luckily, they had preserved some of the remains in anticipation of foul play. Brennan discovered that Cooper had been murdered with an experimental antacid while in the hospital for cancer treatments.

Booth and Brennan paid a visit to an old FBI agent (Rance Howard) who had information on the Cooper cover-up from years before, but before they got anything out of him they were called to a crime scene. Sweets had been attacked while retrieving a document that was evidence in the case. With Brennan and Booth kneeling over his body, the fan favorite character and soon-to-be-father died in their arms.

In the next episode, Booth, Brennan and the rest of the team will have to deal with the loss of their close friend while still trying to solve the conspiracy case. They had better hurry, as things only seem to be getting more dangerous for everyone on the case. "Bones" fans will have to tune in next week to see what happens.

What did you think of the “Bones" premiere? Tweet your thoughts to @Ja9GarofaloTV.