1897年，大韩帝国时代动荡混沌，时有不同罪案发生，别巡检调查队四出调查，找寻破案的线索。 别巡检第2季的时代背景为1897年大韩帝国的国号宣布之后，比第1季还要迟些。高宗自俄罗斯回国后自称为皇帝，由此朝鲜便变为帝国，以阐明国家的自主性和独立性。并且施行了财政、教育、军事等几乎全方位的光武改革，令朝鲜向现代化迈进了一大步。因此这个时期应该是比第1季更为激动人心的时期，然而大韩帝国所追求的新价值，让国民看到的却是比任何时候都强大的同一与自主的混乱。
有一天，馬古路星人及孿生怪獸來襲地球。當時身任地球防衛隊MAC的隊長諸星團，立即變身為賽文奧特曼迎戰。但不敵，幸得雷歐奧特曼現身相助，才合力把怪獸趕走。
With Lidsay and Bobby's help, Jimmy defends his personal friend, dentist Henry Olson, when he is tried for murdering a woman who was fount dead in his chair. Hostile ADA Richard Bay tries to prove the two were having an affair, when in fact their relationship was a lot more complicated than he could possibly imagine. Meanwhile, decapitator George Vogleman returns, asking for Ellenor's help when his co-op serves him with a eviction notice.
Gibbs和他的调查组着手调查一起牵连海军罪案调查处特别探员NickTorres（新常规演员WilmerValderrama）的汽车爆炸案——Nick六个月前在阿根廷执行深度卧底任务时神秘失踪。Gibbs接连拒绝了八名填补DiNozzo职位空缺的人选……其实他早就看上了海军罪案调查处特别探员AlexQuinn（JenniferEsposito），非她不要！DuaneHenry扮演的军情六处特工ClaytonReeves从本季开始成为常规角色。
