Five months later. Sydney quits the CIA and joins a Black Ops unit called "Authorized Personnel Only" alongside Dixon, Jack, Vaughn and... Sloane whom for limited immunity is co-operating with the APO. Meanwhile, the truth Sydney found out in Wittenberg endangers her relationship with Jack, and eventually she reveals the awful truth to Vaughn: about her father having Irina murdered over a year earlier.

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。

Five months later. Sydney quits the CIA and joins a Black Ops unit called "Authorized Personnel Only" alongside Dixon, Jack, Vaughn and... Sloane whom for limited immunity is co-operating with the APO. Meanwhile, the truth Sydney found out in Wittenberg endangers her relationship with Jack, and eventually she reveals the awful truth to Vaughn: about her father having Irina murdered over a year earlier.

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。

丹尼（塞缪尔·杰克逊 Samuel L. Jackson 饰）是一名出色的谈判专家，屡立战功。当他的人生顺风顺水时，刹那间的转折让他措手不及。他的搭档发现警局内有人私吞公款，却在打算告诉丹尼实情时惨遭杀害，第一时间赶到现场的丹尼自然最大嫌疑人。当他确信是警局内有人要找他做替死鬼，百口莫辩之际，他铤而走险绑架了内务监察部检察官和其助手等人，想通过与警方的对话为自己洗刷罪名。