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Shortly after a Cylon nuclear weapon strikes Galactica in the initial wave of the Cylon attack, Kelly begins giving orders to aid crewmembers trapped or fighting damage in the port flight pod, where the detonation occurred, after Executive Officer Saul Tigh hesitates. Tigh soon countermands Kelly and orders the flight pod vented to stop the fires. He also assists in the capture of Aaron Doral (Miniseries).
When Commander Adama is shot by the Cylon infiltrator Sharon Valerii, Lieutenant Felix Gaeta reminds him on his arrival to CIC that Kelly is now second-in-command (Scattered). As a strong believer in Commander Adama's philosophy on computer networks, he voices his objections over networking Galactica's computer systems after the battlestar loses the Fleet due to incorrect jump coordinates, asserting that the Old Man would never even consider Gaeta's option to network the computers for a faster jump calculation. Soon after, when Galactica is boarded by Cylon Centurions, Kelly assists Lieutenant Gaeta and Colonel Tigh in coordinating an effort to stop their advance (Valley of Darkness).
Captain Kelly apparently returns to his day to day duties as LSO, coordinating Viper landings from the port hangar bay, as Commander Adama returned to duty and the normal chain of command was restored. He is on duty when Louanne Katraine, disoriented from stims, crash lands her Viper onto the landing bay (Final Cut).
When the trial of Gaius Baltar draws near, Kelly tries to disrupt the proceedings with a series of bombings. One of the attacks kills Baltar's lawyer. An attack on his next lawyer, Romo Lampkin, is thwarted only by chance. A third attack injures Lampkin. When questioned, Kelly says that he couldn't handle sending off pilots to their deaths anymore, and would continue to try if he is not locked up (The Son Also Rises). Because of this, it is unlikely that he is currently on active duty in his role as LSO.
After the discovery of a devastated Earth (and after being freed from the brig by the mutineers), he joins Felix Gaeta's mutiny and leads a squad of marines in pursuit of Admiral Adama and Colonel Tigh. (The Oath)
He later went to Colonial One, where he heard two marines gun down the Quorom of Twelve, after he is given an order by Zarek. He returns to Galactica, where he defends an arms locker and runs into Tyrol, who comes out of the air vents. At first, he contemplates killing him, but after a discussion, he lowers his rifle, before raising it again and tells Tyrol to leave. Tyrol escapes into an air vent again. Later, Kelly is ordered to escort Adama to his execution with some marines. However, Kelly splits off from the rest of the group. Knowing what is about to happen, he breaks down in the memorial hallway, where he encounters Lee and his group. Aaron decides to defect and not only tells the team where Adama is to be executed, but assists them in rescuing him. Kelly takes part in Adama's recapturing of Galactica as well. (Blood on the Scales)