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>>
Friday, July 25 2014 8:59 PM EDT2014-07-26 00:59:16 GMT
3 indicted in Arizona bestiality case
A man in jail on bestiality charges was re-arrested Wednesday on suspicion of burning his initials onto the private parts of at least one woman making her as "his property," Arizona authorities said. More >
Christopher Jackson, 49, of Chandler, was sentenced to three years of supervised probation for two counts of bestiality.More >