布朗医生(特里特·威廉斯 Treat Williams 饰)带着儿子艾弗拉姆(格里高利·史密斯 Gregory Smith 饰)和女儿达利亚(薇薇·卡登尼 Vivien Cardone 饰)来到了雪山镇,尽管这里风光秀丽风景宜人,但这美好的一切并没有治愈布朗医生心中的伤痛。原来,曾经的布朗医生是一名工作狂,一心扑在事业上的他忽略了自己的家庭,而他的冷漠和大意便是直接导致其家庭破碎的罪魁祸首。如今,心中充满了悔恨之情的布朗医生来到了妻子朝思暮想的雪山镇,在这里,他决心再给自己一次机会扮演好“父亲”这个角色。然而,他的儿子和女儿会接受他的“回心转意”吗?又会有怎样的故事发生在这座表面平静实则激流暗涌的小镇之中呢?
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。
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.'
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.
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.