A 2-year-old from Smithtown and his father, who is believed to have abducted him, were found in a car on fire Wednesday – both with bullet wounds – in Virginia, according to Rockbridge County Deputy Tony McFadden.

Suffolk police say the toddler, Jovani Ligurgo, who was reported missing by his mother Tuesday afternoon, was discovered in John Ligurgo’s Jeep Cherokee in the residential neighborhood.

It wasn't immediately clear if the gunshots were the cause of death. An autopsy is scheduled for Thursday.

The course of events that led to the tragic end began Tuesday around 3:30 p.m. when police responded to a 911 call about a fire at the Brettonwood Condo complex in Coram. Police believe the fire started in Ligurgo's second-floor bedroom, but he and his son were not in the apartment.

An hour later, Jovani's mother Maria Busone called police because her son had not yet been returned by John Ligurgo per a family court visitation order. She then drove to the condo after hearing about the fire and told police that he might be armed with a hunting rifle.

Suffolk police say that's when they began a missing persons investigation, but no Amber Alert was issued at that time. There was also no alert to local media until after midnight.

The vehicle's description along with the missing persons information was entered into NCIC – a national alert system that's only accessible to law enforcement.

Suffolk Police Commissioner Geraldine Hart said that at 7:30 p.m., the NYPD alerted Suffolk police that the vehicle had entered New Jersey.

“We notified New Jersey and Pennsylvania police of the effort to locate the vehicle,” said Hart.

But at 8:45 a.m., Suffolk police were notified that Ligurgo’s vehicle was found with two occupants dead inside.

Busone and Ligurgo were scheduled to meet Thursday for a custody hearing.

Neighbors also told News 12 that John Ligurgo had just lost his job a few days ago.

A GoFundMe page has been set up to pay for Jovani's funeral expenses.