McQueary says Johnson, his former live-in girlfriend, told him, "You made me do this."
She told Logan she suffocated the child and put him in a diaper bag in a trash can.
But two years later, McQueary now believes that was the last time Johnson actually told the truth.
As much as it pains him, he tells CBS 5 that he's accepted that his son is likely dead.
"I always knew the evidence was there in the things that police and the FBI told me and listening to the interviews and stuff that Elizabeth said, but I guess I never really wanted to believe it and I guess just over time I came to the realization that this might be exactly what Elizabeth did," McQueary said.
But that acceptance hasn't made living any easier. Gabriel has now been missing longer than McQueary ever knew him alive and the lack of answers still haunts him daily.
"There are certain days where I don't want to get up and do anything and that's all I think about, and some nights I just lay there in bed and think about it and can't sleep."
"There was chances that I had where I could have taken Gabriel away from Elizabeth and wouldn't be in the situation where I'm at right now, and I still think about that and I think that's one of my problems too."
Johnson still sits behind bars unwilling to help investigators or even her own lawyers. The third defense team abandoned her earlier this month.
"It was necessary because the relationship with Ms. Johnson at this point is just broken and actually has been all along," said Marci Kratter, Johnson's former attorney. "As we've told the court and the prospectors, we know no more about this case now than when we took over."
Her attorneys continue to claim Johnson is mentally unfit, but McQueary said he knows better.
"Elizabeth always looked out for herself and I think that's what she's doing right now and that's what she has been doing all along," McQueary said. "I think she did do what she said she did and that's why she's not talking to anybody."
"If Gabriel was alive, I think she would have talked by now. I think she would know she has a chance to get out of jail sometime in the near future or get served and get released if we found Gabriel right now if she just told the truth," McQueary stated.
He has since moved out of state to try and move on with his life. But a small part of him still prays for a miracle.
"I still hold hope that he's still out there and I wish and I pray that someday he'll pop up somewhere and I can meet my son as a grown man or a teenager or even a year from now," McQueary said.
"I'd probably have a smile on my face but I'd be crying at the same time."
Johnson's next court appearance is scheduled for Jan. 6 when she'll get her fourth attorney.
She claims she gave Gabriel away to strangers in a Texas park.
She is facing charges of kidnapping and child abuse.
READ: Baby Gabriel's father pleads guilty to theft (4/16/2012) Judge tosses evidence in 'Baby Gabriel' case (4/16/2012) Father of missing Arizona baby to testify (4/12/2012) 2 women about to faceMore>>
Sunday, March 9 2014 3:04 PM EDT2014-03-09 19:04:53 GMT
(Source: CBS 5 News)
An administrative law judge with the NTSB ruled Thursday that the FAA has no decision making authority over the operation of unmanned aerial systems (UAS, also known as UAVs or drones) temporarily clearingMore >
An administrative law judge with the NTSB ruled Thursday that the FAA has no decision making authority over the operation of unmanned aerial systems. More >
Sunday, March 9 2014 7:36 PM EDT2014-03-09 23:36:20 GMT
Car over the edge of I-17 in Phoenix
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Arizona Department of Public Safety officers investigated a bizarre crash Sunday on Interstate 17.More >
Sunday, March 9 2014 7:59 PM EDT2014-03-09 23:59:38 GMT
Buckeye shooting leaves one dead
Buckeye police are looking for a suspect who shot a tow truck driver early Sunday afternoon and then fled. Officer Tamela Skaggs said the suspect was last seen heading west on MC85. She said the truckMore >
Witnesses said they heard somewhere between four to five gunshots and found a man lying on the side of the road in front of Don Lalo Auto Repair.More >
Monday, March 10 2014 6:34 PM EDT2014-03-10 22:34:40 GMT
Family, friends and the community will gather Monday to honor the Phoenix police detective who died in a gun battle with a fugitive. The Phoenix Police Department announced Wednesday that funeral servicesMore >
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Sunday, March 9 2014 10:04 AM EDT2014-03-09 14:04:05 GMT
Reported kidnapping in Phoenix
A woman was kidnapped at gunpoint Saturday evening, Phoenix police said. It happened near 67th Avenue and Coolidge. Officers said she was walking northbound on 67th Avenue when a car came up behind her. PoliceMore >
Police released a grainy video of what they said was a kidnapping on 67th Avenue near Coolidge. The video shows a woman being thrown into a white car Saturday afternoon. More >
A 45-year-old man is dead after a cab struck him in Scottsdale early Sunday morning, police said. The man had left a nearby restaurant before 1:30 a.m. and walked across Scottsdale Road, said ScottsdaleMore >
The man had left a nearby restaurant before 1:30 a.m. and walked across Scottsdale Road, said Scottsdale police Officer David Pubins.More >
Friday, February 28 2014 3:27 AM EST2014-02-28 08:27:54 GMT
On a rainy Monday afternoon, the buzz of air-powered tools rattled through the garage at CSC Lifts, Liners, and Accessories. The experienced hands of Darrell Carmena applied just the right pressure toMore >
A truck, the man of men, holds so many memories for a family. This fitting tribute is a chance to live on through the work, the sweat and the mud.More >