AFL chief Gillon McLachlan has revealed the Australian Sports Anti-Doping Authority has gathered "a lot" of evidence since ending its joint investigation with the AFL in August last year.
This suggests Essendon's players could face an increasingly prolonged fight to clear their names.
The Bombers and suspended coach James Hird are fighting to have the initial joint probe, which culminated in an interim report last August, deemed unlawful by the Federal Court.
Before Friday's directions hearing, Justice John Middleton has told lawyers representing the club and Hird they need to file an outline of any further evidence they have by Wednesday afternoon, having submitted their originating applications last week.
This could include whether there has been a statement of facts agreed between the parties and an indication of possible trial dates and whether any subpoenas or affidavits will be required.
Justice Middleton has said he wants to set down a date for a trial on Friday and is hopeful of eventually dealing with the case as to whether the joint investigation by the AFL and ASADA was unlawful with "some expedition".
That is welcome news for Essendon, Hird and the 34 current and former players who have been issued show-cause notices, but a court date could still be at least two months away.
But even if Hird and the Bombers are ultimately successful, and the show-cause notices are deemed illegal, ASADA has continued to build its case.
This could allow it to reissue show-cause notices backed by fresh, independent evidence, a point ASADA chief executive Ben McDevitt has suggested. This, though, would almost certainly not include interviews with players.
McLachlan said he could not say whether players would ultimately escape penalty.
"We don't know what the evidence is,'' he said. "I know what was in the interim report, but there is a lot that is going to be relied upon, as I understand it, [a lot of evidence has been] gathered since then," he said.
Players have until July 11 to respond to show-cause notices but that could be influenced by Essendon's bid for an injunction and also its case over the legality of the investigation.
The specific meaning on what constitutes a "joint" investigation will be crucial.
One lawyer not involved in the case says ASADA, an independent body, could argue that when interviews were conducted it was working purely on the anti-doping side of the case, with the AFL only interested in governance matters, therefore each was not working hand in hand.
ASADA maintains it is on safe legal ground, with one part of its act giving it the power to do "all things necessary or convenient" to uphold the national anti-doping code.
Claims there was a sweetheart agreement in place for players to escape penalty under a "no-fault or negligence" defence because they had been duped - meaning ASADA would give "favourable consideration" at the time of sanction - did not constitute a promise and would be difficult to prove, lawyers not involved in the case believe.
Lawyers also point out Justice Middleton could decide to rule only some of the evidence inadmissible, therefore the case could proceed.
In their application to the Federal Court, the Bombers believe the joint probe was "ultra vires" (beyond the scope) of ASADA's powers under the act and the National Anti-Doping Scheme, and claim ASADA staff and AFL employees during the interview process "represented the investigation as a joint investigation" and players were "compelled to provide information".
McLachlan said he did not know when there would be a resolution, because "there are so many variables".
He said on Fox Footy's On The Couch the AFL had no "visibility" on the discussions between ASADA and the lawyers representing the players.
ASADA has angered players by appearing to offer them the chance to come forward and admit they had unwittingly been injected with a banned substance - Thymosin beta 4 - by sports scientist Stephen Dank.
The players believe they were not administered anything illegal. Dank maintains he has done nothing wrong and injected players with the permitted Thymomodulin, an immunity booster safely given to infants.
"At some point, potentially the ball comes back to us [AFL], but I don't really have a line of sight of when that is going to be," McLachlan said.
He confirmed the AFL had a "doomsday" contingency plan should players be listed on the Register of Findings and ultimately receive infraction notices, and the Bombers were forced to seek replacement players.
"I am not going to get into the specifics ... because I don't think it's appropriate to speculate because there are a multitude of scenarios. There could be no players, there could be 20 players," he said.
"If there is , all I can say to you is we have workshopped from the very start every possible scenario and I am comfortable ... that we would be able to get through in the worst-case scenario if that happened."
The AFL needs to retain 18 teams as part of the broadcast-rights deal that bankrolls the league. One contingency plan could be giving the Bombers access to a special draft of players in state leagues.