All three maintained their innocence since the allegations came to light and throughout the investigation.
In Tuesday night's press conference, McLachlan said the league had come to an "imperfect resolution" with an agreement reached between all parties.
Fagan, who was an assistant under Clarkson at the Hawks, released a statement in the aftermath of the league announcement, saying it provided closure in what has been a difficult time.
"The investigation has now been terminated, with the agreement of the complaints and the investigation panel. It is right that this should occur. It is long overdue.
"I have maintained my public silence on the issues raised publicly because I was bound to confidentiality by the rules of the AFL investigation. It has been a very distressing several months for me since these allegations were first you published by the ABC without the investigation that was conducted having asked for my version of events.
"I am innocent of any of the allegations made against me and always have been.
"I have been in footy for a long time - most of my life. In that time I have had the interests of the welfare of my players as my foremost consideration. I have treated all players with equality and fairness.
"I have always respected the tremendous contribution that First Nations people have made to our game and I respect them greatly. I always have. I always will. And I am conscious that this fact of a process cannot have been easy on those First Nations people who were complainants. Those whom I knew, I hold no grudges against and hold only a wish that whatever pain they are suffering can be healed over time.
"The combination of the AFL investigation, the ABC article, that was published making very serious allegations against me, and the leaks that have occurred to the press, have amounted to a travesty of justice. It has caused tremendous hurt to me those who care about me, and other people whom I know to be innocent of wrongdoing, such as Clarko and Jason Burt. These are fine men and they have been publicly shamed by false allegations.
"The complainants, the investigation panel and the AFL have agrees that no adverse findings have been made against me, Alastair Clarkson and Jason Burt, and that no charges will be brought against any of us under the AFL Rules. It has been further agrees by the complainants, the panel and the AFL that the matters the subject of the investigation will not be investigated further by the panel.
"These matters are also fully justified. I have always categorically denied all of the allegations against me. The allegations are false. I am completely innocent. I have never deviated from that position as I knew from the beginning that the allegations were false. I have never had my chance to publicise my position on the allegations that the ABC chose to air publicly.
"Prior to the agreement refereed to above being reached, the documents held by Hawthorn that the complainants had refused to release to me were released to me, very recently, with their consent. Those same documents were in the possession of both the investigation panel and the AFL for consideration by those parts for a significant time period to their release to me. I am bound by a confidentiality deed not to disclose the contents of the documents. But I can say that they support the categorical denials of the allegations against me that I have stated from the outset. I can also sat that for my part, I would be completely happy for all of these documents to be made public.
"I am happy for any of my conduct and any documents to be aired publicly in a public court of proper public process and let someone impartial decide what is true and what is false.
"I am not a party to the agreement between the complainants, the investigation panel and the AFL. But I stand vindicated by it.
"I have made no concessions. There are none to make. I have always vigorously defended myself, and will always do so, as I have done nothing wrong.
"I am proud of my record, built up over four decades, of nourishing not just the football career but also the lives of the young people I have coaches. This includes all of the First Nations players I have been fortunate enough to coach.
"I have from the start received countless messages of support., including from very many First Nations players I coached at Hawthorn, Melbourne and now at the Brisbane Lions. I wish to take opportunity to thank all of the people have supported me. The investigation has taken a very damaging toll."