After 166 games at three clubs - Geelong, Melbourne and the Brisbane Lions – the powerful midfielder called time on his career on Monday after a season derailed by an Achilles injury.
It was true new Lions coach Justin Leppitsch wanted to blood younger players and that was part of the reason Moloney hadn't played since round five, but the issue ran much deeper.
Since the pre-season, the 30-year-old has tried to manage the debilitating injury.
He'd had eight epidurals over the season to numb the pain, tried cortisone, a traumeel injection and a PRP (platelet-rich plasma) injection in an attempt to get it right.
But nothing has worked.
Moloney was dropped to the Lions' NEAFL team and did little to impress, unable to burst clear from stoppages like he could at his best.
He knew last week his time was up.
"I tried to train on Thursday and I just couldn't run, couldn't get out of first gear," he said.
"It was a frustrating one, but that was the answer for me. That told me I couldn't go on and that I was going to retire.
"The Achilles injury made the decision easy. I just can't run any more."
Moloney's career was at the crossroads after the 2012 season following a falling out with then-Demons coach Mark Neeld, but he quickly fitted in at the Lions.
He was extremely popular among the playing group and always one of the first mentioned when younger players were asked who had influenced their time in Brisbane.
Moloney said the Lions had offered him a send-off game, but his body was not even able to get up for that.
"Unless you've had an Achilles injury, people don't understand. You can't push off," he said.
"If you want to play AFL, it's (a) repeat speed game and you've got to be able to get to contests and I just can't do that.
"It's a huge relief really. The whole year has been a frustrating one. I've tried to keep positive because I want to leave a legacy at the footy club that it's good to help other players no matter what situation you're in."
He admitted to having some tense words with Leppitsch over the season, but was adamant their relationship was as strong as ever.
Moloney said despite the frustrations, he loved every minute of his two years in Brisbane.
"The direction Leppa's going is the right one, playing younger guys and they're showing a lot. They've been fantastic since they've come in.
"I understand the direction he's going in. For myself, I just couldn't run, couldn't compete with the best of them and that's what you've got to do week in, week out.
"We had some heated conversations, but that was frustration from me.
"He was asking me to do things I couldn't do any more and that's the problem when you get to 30 and carrying injuries. It's a ruthless industry.
"People want the best out of you and if they're not getting that they're asking questions - 'why not?' We had some heated conversations but our relationship is fine. We respect each other."
With his playing days now over, Moloney said he would return to Warrnambool for a week to see his family and consider his future.
He seems a ready-made coach with his instinctive teaching ability.
Moloney already mentors Ryan Lester – the man who has effectively taken his spot – and is best mates with teenager James Aish.
He said he would take time out and consider all options though.
"I'd like to be remembered as an honest guy and a good teammate," he said.
"I've got nothing left. I always took pride in the way I trained, always pushed myself and pushed others to get the best out of them. I left no stone unturned."
Twitter: @AFL_mikewhiting
