California Highway Patrol says the child has been safely found.
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The suspect accused of abducting the boy was 30-year-old Joshua Yago.
Yago and the child were found early Saturday morning in Hayward by the Hayward police department.
Authorities activated the alert for Alameda and Contra Costa Counties Friday evening.
Police say the child was taken after a double shooting in Sacramento Friday afternoon.
A man and woman suffered non-life-threatening injuries.
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The suspect took the woman's three-year-old child and believed Yago was on his way to San Jose.
It's unclear what the relationship is between the suspect and the people shot.
Yago is currently in custody and booked on charges related to the kidnapping and double shooting.
There is a family court case against Yago in the Sacramento Superior Court.