Ethan Rickover (also referred to as simply "The Judge") was a judge on the California Court of Appeals; at the time he was earmarked for appointment to the state Supreme Court, he was also, finally after twelve years, discovered to have been the one responsible for the murder of Trudy Monk.
Though only appearing in the last two episodes, his character was hinted at far in advance and Rickover fills the role of the true, hidden main antagonist of the entire show for his main role in Trudy's death, which basically ruined Monk's life.
A succesful lawyer, Rickover taught law at UC Berkeley during the early 1980s. While there, he seduced one of his students, Trudy Ellison, who became pregnant with his child. Rickover was married at the time, but deceived Trudy about this fact. To conceal the affair, he also told Trudy that the child had died shortly after her birth, and (presumably) bribed the midwife who oversaw the delivery, Wendy Stroud, to corroborate this. He and Trudy would have no contact for another ten years.
Rickover was appointed (or elected) to the state superior court a short time later.
In 1997, Rickover was a candidate for the Court of Appeals and was mentioned in several news stories. He was contacted by Stroud, who told him that she had found religion and was not going to lie for him any longer. To protect his position, Rickover murdered Stroud and buried her body in his backyard. Afraid that Trudy might try to expose him, he contacted her out of the blue and lured her to a meeting. He hired a criminal, Frank Nunn, to plant a bomb in her car. Nunn hired Warrick Tennyson, an explosives expert, to build the bomb for him. The plan worked, and Trudy was killed.
Nunn referred "The Judge" in connection with Trudy's murder in an old letter, which was found in his apartment after Nunn's death. Twelve years later, in 2009, Rickover was on his way to the state Supreme Court, when his past reared its head again. Dr. Malcolm Nash, the director of Wendy Stroud's birthing clinic, found a reference to the child while transferring the clinic's old paper records to computer files. He contacted Rickover, possibly trying to blackmail him, and Rickover hired another killer to dispose of him. When the SFPD, with the help of Adrian Monk, began to close in on the hit man, Rickover hired the man for an additional job - killing Monk - because he knew full well that Monk would pursue him relentlessly if he connected Rickover with Trudy's death. But the plan backfired: Monk was almost killed by a slow-acting poison administered by the hit man, but, believing he was dying, decided to finally open a parcel Trudy had left for him the night before she died, which turned out to contain a videotaped message revealing her affair with Rickover and that he was the one she was supposed to meet.
Though Rickover denied everything, Monk escaped from a hospital and caught Rickover in his backyard late at night, forcing him, at gunpoint, to dig up Wendy Stroud's corpse in his backyard. Exposed, Rickover confessed. Monk was tempted to gun him down then and there, raging at him that he had murdered two innocent women just to safeguard his lofty position.
Presumably unwilling to end up in prison because of his role as a judge and feeling that his life was over (and perhaps finally feeling the shame of what he'd done), Rickover snatched up Monk's pistol and committed suicide, shooting himself in the head.
Just before he pulled the trigger, Rickover shouted at Monk to "take care of her!" a clue that led Monk to realize that Trudy's daughter was still alive. This suggested that he had been keeping tabs on her throughout her life.
Rickover was a cold-hearted, ruthless man who was willing to get rid of literally anyone in the way of his path to becoming a powerful judge. It was likely that Rickover's dream was to be on the state Supreme Court (possibly even on the national Supreme Court) and he was unwilling to let anything in his past rear up its ugly head and threaten his success and chance at glory. In addition to being an egotistical narcissist who was willing to seduce his students and abuse his power as a college professor, Rickover was also a liar (even if it meant lying about the birth of his illegitimate child to her mother or even going as far as to slander a dead person's name) with no remorse for his actions. It is unclear how many of his students Rickover seduced and took advantage of, but it is unlikely that Trudy Monk was the only victim of this abuse of authority.
Being a judge did not mean that he upheld the law, however, as Rickover was a corrupt killer who was indirectly responsible for at least three deaths, the deaths of Trudy Monk, Wendy Stroud and Dr. Malcom Nash. He also attempted to poison Adrian Monk with his hand wipes, which inadvertantly ended up poisoning Natalie Teeger as well. Had both not gotten the antidote for the poison, they, too, would have died. It is unclear if Judge Rickover was responsible for other murders as well, but it's certainly possible given how many hitmen he knew and his sordid past of affairs and corruption. It would not be until he was much older that Rickover would finally pay the ultimate price for his many crimes. Rickover also was responsible for ruining Adrian Monk's life by killing the most important person in his life, which was the trigger for Monk's crippling anxiety and severe Obsessive-Compulsive Disorder.
Up to the end, Rickover was still holding his power over people by attempting to tell Monk that he did not want to kill a judge, only for Monk to tell him that he was now the judge. Despite being the main antagonist of the entire show, Rickover was responsible for Monk turning to detective work in the wake of Trudy's death and solving hundreds of homicides. Rickover also presumably kept tabs on his biological daughter throughout his life and was shown to be married (though he cheated on his wife at least once and it is unclear how many times he was married).