Hird has claimed Justice John Middleton had "erred" in failing to identify "any source of power" why ASADA had been allowed to conduct a joint investigation with the AFL into Essendon's 2012 supplements program.

In his 10-page notice of appeal lodged in the Federal Court on Thursday, Hird and his lawyers have revealed their grounds of appeal, what findings Middleton should have made, and their orders sought.

While the Bombers have decided to not appeal to the full Federal Court, with chairman Paul Little confirming he had wanted Hird to follow the club's path, Hird said he had felt compelled to take a stand.

"I have not taken this decision lightly. I believe this is the right course or action and is in the best interests of the Essendon Football Club, its players, the supporters and the game," Hird said on Thursday.

"The short-term simple approach would be to acquiesce and plead guilty to ASADA even though the players, the club and myself do not believe we have breached the rules. It would be a lie as would pleading out of the proceedings when I, my lawyers and the Essendon Football Club lawyers firmly believe that the investigation was conducted unlawfully and an appeal will be successful."

Hird said he had wanted to appeal because "this is the proper and appropriate course to vindicate the legal rights of the EFC and its players".

"The challenge to the lawfulness of the joint investigation was, and is, an important step in showing that the Essendon Football Club, its players and staff were submitted to a compromised investigation and were treated unfairly. If we don't appeal our players may be stained forever by the innuendo, misconceptions and falsities that resulted from an investigation that we believe was conducted unlawfully," he said.

"It is important that an investigation based on unlawfully gathered information never occurs again to any person, sporting club or organisation."

After a three-day trial before Middleton in August, the judge gave his orders last month, declaring the probe by ASADA and the AFL into the Bombers' supplements program had been lawful. This meant a bid by the Bombers and Hird to have the show-cause notices issued to 34 present and former players quashed had failed.

However, Hird is still confident of having the show-cause notices already issued, and the revised notices set to be delivered complete with evidence alleging the players were administered the banned peptide, thymosin beta 4, scrapped.

"The primary Judge erred in making the following findings," Hird's lawyers wrote in the notice of appeal.

"That the respondent [ASADA chief] and the Australian Sports Anti-Doping Authority did not exceed their powers under the Australian Sports Anti-Doping Authority Act 2006 [the Act], the Australian Sports Anti-Doping Authority Regulations 2006 [the Regulations] and the NAD Scheme ... by deciding to conduct, and conducting, an investigation jointly, or in close cooperation, with the Australian Football League into the Essendon Football Club, the Appellant [Hird] and the players who were on the EFC's playing list during the 2012 football season.

"The primary Judge failed to identify any source of power in the Act, the Regulations or the NAD Scheme that enabled the Respondent and ASADA to agree with the AFL to conduct, and then to constitute and conduct, an investigation jointly, or in close cooperation with, the AFL."

Hird maintains the 2013 interim report that ASADA presented to the AFL was used "for purposes that were extraneous" to an anti-doping investigation. This report played a part in Hird receiving a 12-month suspension and the Bombers being find $2 million for governance failures.

Hird also maintains ASADA had "breached their statutory obligations of confidentiality" during the interview process with players and officials, when AFL investigators also sat in on the interviews.

Hird wants "a declaration that the joint investigation conducted by the Respondent [ASADA chief] and ASADA jointly with the AFL into the EFC, the Appellant (Hird) and the EFC players was ultra vires".

He also wants a permanent injunction against the current show-cause notices or "any further notice" the players could be subjected to. However, he has not sought an injunction against ASADA reissuing the notices in the meantime, which it is planning on doing. There are still about 20 players at the club who were part of the 2012 program. Some players told Hird they did not want him to appeal Middleton's decision.

"If we don't appeal, our players may be stained forever by the innuendo, misconceptions and falsities that resulted from an investigation that we believe was conducted unlawfully," Hird said.

"At no time during the 2012 season, did I believe any Essendon player was exposed to any supplement or drug that fell outside the wider ASADA or AFL code.

"Two years since the end of that season, I still do not believe any Essendon player took anything illegal and no one has shown me any evidence that would lead me to believe differently.

"I am extremely sorry for the pain this saga has caused the players of the Essendon Football Club, their families, the Essendon Football Club staff, the Essendon Football Club supporters and the football industry as a whole.

"I am requesting expedition of this appeal and will not ask for a stay of the notices.

"The players and ASADA will be able to continue with the show-cause process whilst a full court deals with the legality of the investigation."