Lt. Singer's body was found up on a tree near a river. The body was somewhat decomposed and her face was basically gone (crows ate through it).
A team (not the JAG team) was sent to investigate and gather clues and evidence, a la CSI. At first it seemed that the body had been there for about 3 weeks and that the woman was about 4 or 5 months pregnant (before they knew it was Lt. Singer).
After running DNA tests and doing the autopsy, they were sure that it was Lt. Singer.
The investigative team went to JAG headquarters to ask some questions and Harm got all defensive, maybe because he feared that his half-brother (Sergei) would be accused since he had a relationship with her and since there was a possibility that he could be the father of her baby.
Anyway, none of them knew about Sergei's relationship with her, only Harm. So because of his behavior, right away the team suspected Harm himself.
After going through the body, a napkin was found on her with a phone number from Moscow. They matched it to Sergei and also figured out he was Harm's half brother.
They brought Harm in for questioning but couldn't officially arrest him because they had no evidence that he had contact with Lt. Singer prior to her murder.
When they brought up Sergei and the napkin to the conversation Harm in trying to protect his brother, right away told them that it was him that gave Singer the napkin. That was the connection that the investigative team needed and charged him with the act of murder on the spot.
BTW, it looks like they're trying to create a spin-off series with this new team. All of them are known actors (although I don't know their names but I have seen them before) and also they got most of the screen time.
Kind of like the CSI episode where one of the cast goes to investigate a case in Miami and we're introduced to another cast which soon became CSI: Miami.