Having woken up in Hong Kong, with no memory for the last two years (!), Sydney returns to Los Angeles to try to piece together the last two years of her life and discovers the fates of her friends and family: Vaughn has married thinking that Sydney was long dead; Marshall is having a baby with CIA tech expert Carrie Bowman; and Dixon is now the new division head of the L.A. office branch of the CIA. Sydney also learns the shocking fates of Jack and Sloane; the former is in CIA custody for communicating with Irina whom still is in hiding, while the latter is living in Switzerland under house arrest in exchange for co-operation with the CIA. Sydney is granted temporary CIA clearance on a case that may help her regain her memory and she meets a new enemy group called The Covenant.

Sydney finds herself face-to-face with her long-lost mother, Irina Derevko, whose intentions for her daughter are made chillingly clear. However, Sydney manages to escape and rejoin Jack and Will in their escape from Taiwan. After arriving back in Los Angeles, Sydney continues her search for Vaughn, not knowing if he is dead or alive after being swept away by a wall of water in Taipei. Will's life is forever changed when he learns the truth about SD-6 and Sydney's life as a double agent. Also, Dixon must decide whether or not to inform Sloane of Sydney's suspicious activities. But Jack intervenes and covers for Sydney who later finds Vaughn who helps her try to track down her mother Irina who's searing for a Rimbaldi artifact called 'the Bible.'

表面上，雪莉（珍妮弗·加纳 Jennifer Garner 饰）是一名普通的大学研究生，实际上，她已为名为SD6的秘密情报组织工作多年。在同男友结婚之际，雪莉决定向其公开自己的真实身份，没想到男友却因此被组织的安全人员暗杀。愤怒中，雪莉选择了“罢工”，之后亦遭到了抹杀。危机之中，雪莉知道了自己的父亲杰克（维克托·加柏 Victor Garber 饰）也是和自己一样的秘密特工，并且，在背后扶持SD6的并非国家组织，而是拥有强大武力的反动分子。于私于公，雪莉和SD6都有着不共戴天之仇，她回到了SD6，但此时，雪莉的身份已升级成了为CIA工作的双重间谍，在危险和考验之中，雪莉的任务只有一个，那就是彻底铲除SD6。

在第四季中，世界正处于崩溃的边缘。Victoria Neuman比以往任何时候都更接近美国总统的位置，并受到正在巩固权力的祖国人的有力压制。Butcher只剩下几个月的生命，他失去了Becca的儿子，也失去了他作为黑袍纠察队队长的工作。队员们都受够了他的谎言。众人面临的风险胜过以往，他们必须找到一种合作的方式，在为时已晚之前拯救世界。

在本季中，Tim Speedle离开了，而新人Ryan Wolfe则加入了小组。　　Horatio Caine：David Caruso饰演，是迈阿密达德郡犯罪实验室的组长，曾经是拆弹小组的警官，现在是监识分析师。　　Calleigh Duquesne：Emily Procter演，弹道科学家，出生于路易西安那州达尼尔（Darnell），西班牙语十分流利，曾在图兰大学（Tulane University）获得物理学学士学位。　　Eric Delko：Adam Rodriguez饰演，指纹与药品辨识专家，土生土长于迈阿密，曾在迈阿密大学获得化学学士学位。父亲俄罗斯人，母亲古巴人，所以西班牙语和俄语都很流利。当情况需要时，达可在小组里通常是扮演蛙人的角色。　　Alexx Woods：Khandi Alexander饰演，迈阿密达德郡的验尸官。她有一个古怪的习惯就是在验尸的时候跟尸体讲话，通常是想要让死者死后可以更为安详。　　Ryan Wolfe：Jonathan Togo饰演，是一个想进入真实鑑识工作的基层巡逻员警。他了解到自己永远无法取代史毕的地位，只能尽力地成为小组的一员。沃夫首次出现在“Under the Influence”这一集，不过直到“Hell Night”这一集之后才变成常态演出。　　Yelena Salas：Sofia Milos饰演，一个常常跟CSI一起调查的重案组探员，也是何瑞修弟弟雷蒙的遗孀。