Mark Thompson has confirmed that James Hird was warned by the AFL about the club's supplements program in 2011 but maintains that the league could have intervened in a stronger fashion to prevent the saga unfolding as it has.
The charges against Essendon and four individuals released by the AFL last week claimed that Hird, among other allegations, was warned two years ago by the league's integrity manager Brett Clothier that peptides posed "a serious risk" to the competition.
In the aftermath of the AFL Commission hearing where Hird came to an agreement with the league that he had contributed to Essendon's failure to ensure the welfare of its players, a forthright and candid Thompson said "alarm bells should have gone off in somebody's eyes" after Essendon's decision to follow the path of a controversial supplements program.
"James Hird went and inquired about peptides," Thompson told Channel Nine's Footy Classified on Tuesday night.
"They've sat down, talked to Hirdy, and said 'don't go down that path'. He's gone. We've gone down that path.
"He had the meeting. He's not saying he wasn't warned.
"We obviously went down a path. The alarm bells should have gone off in somebody's eyes."
But the Geelong premiership and senior assistant Essendon coach was firm in his belief that the AFL could have done more to help prevent problems earlier.
"The AFL knew about this problem ... and what I would really like is that if they did know about the problem, come and talk to the club. Come and look inside our club. Ask the questions. It might have been prevented."
Thompson said he had a lot of sympathy for Hird and he knew the club was in for a fight after the coach's solicitor reportedly told Hird to stand down in April.
"How did it get to that? From that point on when he said I thought 'wooo, we're in for a fight here'," Thompson said.
We obviously went down a path. The alarm bells should have gone off in somebody's eyes.
"The way he has been treated ... if people had just been really honest and come up and said 'this is the problem' ... it could have been dealt with better.
"If ever this happens again – any crisis, whether it's Essendon, supplements or another club with another issue, if we don't learn from this situation, then the game's going to be worse for it.
"If the AFL don't talk to us about how to handle it better ... because we were on the other end of it and getting a hammering all year, they'd be silly because we'd have a lot of answers for them."
Several Essendon figures have already called on Thompson to become the club's fill-in coach during Hird's suspension in 2014.
But Thompson said he hadn't given that much thought. "We haven't spoken about it once. I'm not sure what their intentions are. It's hard.
"After the two days I've had, it's hard to think what I really want to do. It has been a pretty intense two days."
The experienced coach also shed some light on his thoughts about Essendon when he returned to Windy Hill before the 2011 season.
"Everyone looks at Essendon as this great club," Thompson said.
"I walked into Essendon (and thought), we’re not a very good club, there’s a lot of areas we need to fix up, let’s get on with this job.
"Not just blaming the board, but … the football department, every part of how we were doing thing wasn’t up to a level that was going to get us back up to the top eight, top four, preliminary finals, grand finals."
Thompson defended the appointment of strength and conditioning coach Dean Robinson, saying no-one had wanted 'The Weapon' to leave when he worked under Thompson at Geelong.
"(Robinson) had the same role at Essendon that he had at Geelong, but Essendon wasn't a good enough club to manage him. That's our whole problem."
Despite the massive damage the supplements scandal had inflicted on the club, Thompson predicted the Bombers would bounce back quickly.
"This is a pretty bad day and it's been a bad year for the club in so many ways .... but on-field we feel like we've done a lot right.
"This is not the end of our season next year, or the year after. If anything it's going to make us stronger."