"Ice Queen"
While chasing after a stray arrow into the forest, a young Boy Scout finds the arrow has landed in a corpse. NCIS agents Leroy Jethro Gibbs, Vivian Blackadder, and Anthony DiNozzo arrive on the scene and meet up with NCIS Medical Examiner Dr. Donald Mallard who informs them that the corpse is that of a pregnant Navy Lieutenant. DiNozzo determine she is a JAG, while Gibbs determines that she washed up from the nearby river.
At the JAG headquarters, Admiral A. J. Chegwidden informs his team that the NCIS has found the body of a Navy Lieutenant, who is believed to be five months pregnant. The team is unable to get in contact with Lieutenant Loren Singer, who is almost nine months pregnant, so they are told that the NCIS plans to use DNA to confirm if the body is Singer's. Commander Harmon Rabb leaves the room causing Chegwidden to wonder aloud if there is something going on between Rabb and Singer.
NCIS Director Thomas Morrow and his team go to the MTAC, where they watch as other NCIS agents successfully capture Amad Bin Atwa. Meanwhile, Dr. Mallard determines that the body is Singer's and was dumped in the river at the top of the falls after being hit with a metal object.
At JAG headquarters, Chegwidden tells his team what the NCIS has found. Chegwidden privately asks Rabb how he is involved with the murder and thinks that Rabb might know who the father of Singer's baby is. Gibbs and Blackadder question everyone except for Rabb, who calls his half-brother Sergei Zhukov to tell him about Singer's death.
DiNozzo finds Singer's car and determines which bridge Singer was thrown off of and gives the evidence he collected to Forensic Scientist Abby Sciuto, who finds Rabb's fingerprint in the car. Dr. Mallard determines that Singer has been dead for three months, Sciuto learns that she called Zhukov before she died, and Special Agent Don Dobbs finds a Navy Commander's hat near the crime scene. After looking up Zhukov's file, they learn about Zhukov and Rabb being brothers. Gibbs interrogates and arrests Rabb, as he believes that Zhukov is the father of Singer's baby and that Rabb killed Singer to cover for his half-brother.
"Meltdown"
Rabb meets with Lieutenant Commander Faith Coleman, who has been assigned as his legal counsel, while Gibbs meets with Major Jack McBurney, who will be arguing against Rabb. Morrow tells Gibbs that he needs him to interrogate Bin Atwa as soon as possible. Sciuto, Dr. Mallard, and Gibbs all testify and Gibbs admits that he no longer believes Rabb killed Singer.
Gibbs, Coleman, and McBurney meet with Sciuto, who tells them that the hat Dobbs found belongs to Rabb. Gibbs interrogates Bin Atwa and uses information Blackadder received from the FBI to get him to reveal information about the location of terrorist Hussan Mohammed. Meanwhile, Abby determines that the hat was planted at the scene recently.
With Gibbs busy on the Bin Atwa case, DiNozzo and Blackadder continue the case without him and learn that Singer regularly met with a man for dinner. Using information from restaurant employees and the JAG security logs, they determine that the man was Commander Ted Lindsey, who Rabb recalls stole his hat. While DiNozzo interrogates him, Lindsey claims that it was an accident and Singer fell off the bridge, but DiNozzo tells him that Singer was thrown off the bridge.
DiNozzo and Blackadder meet up with Gibbs and tell him that Lindsey admitted to everything. They then go with Gibbs to capture Mohammed. They are successful, but Mohammed saw Blackadder and nearly killed Gibbs with a grenade.