Marissa Cortez Wilson (Jessica Alba) memiliki segalanya... menikah dengan seorang wartawan terkenal, memiliki seorang bayi dan anak tiri kembar yang cerdas. Namun pada kenyataannya, mencoba menjadi ibu bagi Rebecca (Rowan Blanchard) dan Cecil (Mason Cook), yang tidak menginginkan kehadiran Marissa adalah tantangan terberat.
Dunia Marissa berubah total ketika maniak Timekeeper (Jeremy Piven) mengancam untuk mengambil alih planet dan Marissa kembali diajak bergabung oleh kepala OSS, mata-mata terbesar dimana maskapai divisi Spy Kids diciptakan. Dengan cepatnya Armageddon mendekat, Rebecca dan Cecil tergerak untuk bertindak disaat mereka mengetahui bahwa ibu tirinya yang membosankan adalah seorang agen hebat. Dengan bantuan teman-teman, Carmen (Alexa Vega) dan Juni Cortez (Daryl Sabara), dan beberapa peralatan canggih, mereka mungkin dapat menyelamatkan dunia dan menyatukan keluarga.
On the surface, Marissa Cortez Wilson (Jessica Alba) has it all...married to a famous spy hunting television reporter, a new baby and intelligent twin step kids. But in reality, trying to mother Rebecca (Rowan Blanchard) and Cecil (Mason Cook), who clearly don’t want her around, is her toughest challenge yet. Also, her husband, Wilbur (Joel McHale), wouldn’t know a spy if he lived with one which is exactly the case - Marissa’s a retired secret agent.
Marissa’s world is turned upside down when the maniacal Timekeeper (Jeremy Piven) threatens to take over the planet and she’s called back into action by the head of OSS, home of the greatest spies and where the now-defunct Spy Kids division was created. With Armageddon quickly approaching, Rebecca and Cecil are thrust into action when they learn their boring stepmom was once a top agent and now the world’s most competitive ten year olds are forced to put their bickering aside and rely on their wits. With a little help from a couple of very familiar Spy Kids, Carmen (Alexa Vega) and Juni Cortez (Daryl Sabara), and some mind-blowing gadgets, they just may be able to save the world and possibly bring their family together while they’re at it.