Harm and Mac are assigned to prosecute three sailors charged with the vicious beating of a man they say raped a fellow shipmate. The rape victim, Petty Officer Lopez, tells Mac that, after an evening of drinking with her three male shipmates, she found herself alone at the bar where they ditched her as part of an initiation into their team. The next morning when she awakened in her car, she realized that she had been raped. When the shipmates heard Lopez's story, they exacted revenge on the man they thought attacked her -- the bar owner. But as Harm and Mac wear down the testimony of the three sailors, a very different story about what happened that evening begins to emerge.

This episode starts with tying up the loose end of Mac being charged in an Article 32 hearing for perjury (People vs. Mac). She is acquitted, thanks to fancy legal-speak from Harm - although she does not have to face a court-martial, she does end being sent up on an Admiral's Mast, which just might be worse.

Mac prosecutes a SEAL jumpmaster is charged with causing the drowning death of a trainee during a parachute mishap by being hung over and is defended by Bud, assisted by a new female Lieutenant who is very ambitious, wanting to be the first female JAG.

Bud & Lt. Singer discovers a safety file that is inadmissible in court that supports the prosecution's contention that the jumpmaster was impaired. The file mysteriously winds up in Mac's car and she thumbs through it. After conferring with Harm who tells her what she already knows, she burns the file. But during questioning court, Lt. Singer objects that Mac is basing her argument based on the file, which Bud reluctantly agrees. Mac is charged with prosecutorial misconduct, removed & replaced by Harm.

Having been chewed out by the Admiral, she takes some leave & heads to spend time with Mic in Australia, running into the Admiral & Dr. Walden who are taking their own weekend 'trip'.

Mac becomes ""Acting JAG"" as Admiral Chegwidden is selected to head the Promotions Board for Captain.

Harm takes up the defense of a former Marine Drill Instructor who is facing life imprisonment under the 3 strikes law.

Cmdr. Ted Lindsey (last seen in ""People vs. Mac"") tries to impress the Admiral & Mac in an attempt to earn promotion to Captain.

Harm and Mac investigate a "collateral damage" incident in Afghanistan when an attack on an Al Queda terrorist kills three innocent civilians. With the help of forensic pathologist Cmdr. Teresa Coulter, Mac and Harm try to find out if any of the remains can be identified as belonging to Al Queda leaders. Meanwhile, when Harm and Mac lose control of their Humvee, they are thrown into a minefield where they're forced to spend the night together figuring out how to extricate themselves from the trap.