Kovac was searching for Booth to kill him for the death of Radik, his father, who was a Serbian warlord. In Bosnia in 1995, when Kovac was six years old, Booth killed Radik during Kovac's birthday party. In 1998, he was adopted after being sent to America via an American Red Cross refugee program when he was eight. Kovac grew up to be a member of the U.S. Military as an EMT by the time he was 28. He took it upon himself to destroy the life of the person responsible for his father's death by targeting everyone Booth loves and the other war veterans in his Army unit. After escaping from prison and bombing the Jeffersonian Institute with the help of his sister Jeannine Kovac, Kovac was tracked down and killed by Booth before his body and jeep were both incinerated in an explosion resulting from a car crash into a nearby ravine filled with gasoline drums.
After solving the murder of Devon Marshall, Booth talks to Brennan about how he killed Radik during his son's sixth birthday party. Booth is particularly saddened at how his son watched his father die in front of him and loved him without knowing who his father was in life.
The body of Aldo Clemens was located at a park with a bunch of balloons next to it. The team discovered that Aldo was tortured for information about Booth. After they discovered where Aldo was murdered, Brennan found an x-ray of someone's skull and Booth realized that it was an X-Ray of Radik's head. Brennan took pictures of the worktable where Aldo was tortured, but Booth rushed her out of there because he located a bomb which exploded, destroying the evidence. It was revealed that Aldo killed himself to prevent giving his assailant any information on Booth. The case remained unsolved, and the murderer was still at large.
The killer that murdered Aldo Clemens was revealed to be the son of Josip Radik, Mark Kovac. He tortured and murdered an old woman to force a delivery man, Michael Reiss, a former Ranger in Booth's army unit, to reveal who killed his father. After he got the information, he dumped her body at Fountainhead Regional Park and started torturing the delivery man just for fun until he eventually died of shock. He sent two hitmen (his father's old bodyguards) to a safehouse where Christine, Hank, and Max were hiding at after finding their location through Max's pacemaker. The hitmen, Goran Milovic and Andre Belgrader, were killed by Max Keenan to protect his grandchildren; however, Max Keenan was fatally wounded and sent to the hospital where he died while recovering from surgery. Booth arrested Kovac after finding out that his defibrillator was used on Reiss to extend the amount of torture inflicted on him as proven by the DNA found on the cord. Kovac asked Booth if he killed his father, but Booth refused to answer while he restrained him.
Kovac escaped from prison with another inmate, Fred Walden, after having outside help from his allies. They killed Fred to avoid being tracked down by shooting him in the head. Kovac's allies used a crate of stolen military grade explosives to break them out of a storm drain connected to the prison that was sealed off by bars. Kovac was able to steal Cam's Jeffersonian ID Card to sneak into the lab and plant the rest of the stolen explosive material beneath the Jeffersonian in an attempt to kill Booth and everyone else in the building. Booth was able to shut down the transponder hidden beneath the Forensic Platform, however it was also connected wirelessly to a radio detonator which allowed Kovac to detonate it if anything happened that delayed the explosion. Most of the workers in the Jeffersonian were able to escape before the explosion however Booth, Brennan, Angela, and Hodgins remained in the building as the explosions occurred.
Despite at least three bombs going off, Booth, Brennan, Hodgins and Angela survived Kovac's bombing, thanks to Booth disarming the bomb under the platform. The group is eventually rescued, but Brennan suffers a head injury that prevents her from being able to remember the clue she found to pinpoint Kovac's location in Fred Walden's remains or to process the evidence. Eventually, Hodgins and Camille Saroyan find the DNA of the person who built the bombs in the one Booth disarmed and identifies the person as Jeannine Kovac who is in fact Mark Kovac's sister, not his wife. Though Jeannine refuses to cooperate, the intern team is able to use Walden's remains to track Kovac to a farm in West Virginia. Driving a jeep and wielding a machine gun, Kovac attempts to kill Booth and Brennan personally with Booth hampered by an injured hand. Moments after Brennan fixes his hand, Kovac drives straight at the two and Booth shoots Kovac in the head, killing him. Kovac's jeep then goes off an embankment into gasoline drums, causing an explosion that destroys his jeep and body.
- Goran Milovic (His father's old bodyguard, sent to kill Booth's family. Killed by Max Keenan.)
- Andre Belgrader (His father's old bodyguard, sent to kill Booth's family. Killed by Max Keenan.)
- Fred Walden (Accomplice in prison escape. Used to get a hideout then murdered.)
- Kyle Capoun (Low-level drug dealer hired to steal Camille Saroyan's ID then murdered.)
- Jeannine Kovac (His sister and partner posing as his wife. Built the bombs used in the Jeffersonian Institute.)
- Unnamed accomplice (Attacked an FBI SWAT team at Kovac's hideout. Killed by James Aubrey.)
- Aldo Clemens (Eaten alive by rats and Aldo later broke his own neck killing himself.)
- Seeley Booth (Attempted to blow up, twice. Survived. Attempted to shoot and run over. Survived.)
- Temperance Brennan (Attempted to blow up, twice. Survived. Attempted to shoot and run over. Survived.)
- Margaret Kwan (Beaten with a hammer and then slit her throat.)
- Michael L. Reiss (Beaten, stabbed, and tortured repeatedly until he dies of a heart attack.)
- Fred Walden (Shot in the head after escaping the prison with Kovac.)
- Jack Hodgins (Attempted to blow up, survived.)
- Angela Montenegro (Attempted to blow up, survived.)
- Arastoo Vaziri (Attempted to blow up, escaped.)
- Cam Saroyan (Attempted to blow up, escaped.)
- Entire Jeffersonian Staff (Attempted to blow up, escaped.)
- James Aubrey (Attempted to shoot. Survived.)
- An FBI SWAT team (Attempted to shoot. Survived.)
Victims by Proxy
- FBI Agent Samantha Chatterbee (Shot to death.)
- Max Keenan (Shot multiple times in the chest; died of his injuries at the hospital after recovering from surgery.)
- FBI Agent Austin Suarez (Attempted, saved by Max.)
- Christine Booth (Attempted.)
- Hank Booth II (Attempted.)
- Kyle Capoun (Shot in the head.)
- An unnamed FBI agent (Shot in the arm by an unnamed accomplice. Survived.)
- Mark is considered to be the final Serial Killer of the entire series and the Main Antagonist of Season 12.
- According to his military records, he was a war hero who served two tours in Iraq as a medic. He was rewarded with a Combat Infantryman Badge and a Bronze Star.
- Kovac is the last person who died in the series.
- He could be seen as the Anti-Aubrey, because both had psychologically traumatic experiences concerning the absences of their fathers that affected the remainder of their lives. Unlike Aubrey who resented his father for everything he did in his criminal career, Kovac was willing to do whatever it takes to honor his father's memory, no matter what crimes his father committed and how illegal his actions.