Officers were called to a house on Glancaster Road, near Dickenson Road, shortly before 3 a.m. Thursday, where they found two men in their 20s with gunshot wounds.
Both were taken to hospital in critical condition.
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One of the men has since died of his injuries and the other has received emergency surgery.
Police say the two men are the sons of Faqir Ali, 63, who investigators say was forcibly taken from the house and likely dragged into an SUV.
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About six hours after the kidnapping, Hamilton police located a man with life-threatening injuries on Beach Boulevard, near the Burlington Canal Lift Bridge and QEW.
Media Relations Const. Indy Bharaj told reporters in an update later Thursday morning that the man has been confirmed to be Ali and remains in a life-threatening condition.
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Detectives say Ali and the other two men targeted were family members living in the household and were not known to police.
Police are expected to be in the area for much of Thursday, probing the scene and probing the neighborhood for potential witnesses and video footage.
Anyone with information can contact the police at 905-546-3843 or leave a tip anonymously at Crime Stoppers.