Essendon faces a massive legal bill after losing its Federal Court challenge against the AFL and the Australian Sports Anti-Doping Authority. The club's legal bill stood conservatively at close to $2 million - although insurance will offset this - before the club on Friday was ordered to pay costs. This was after Justice John Middleton emphatically found in favour of ASADA, ultimately validating the anti-doping body's joint investigation with the AFL into the Bombers' 2011-2012 drug program.

Paul Little's hold on the chairmanship of the embattled club looked tenuous late on Friday after the failure of his bold and costly attempt to take on ASADA. The court decision has left the players in limbo awaiting the next legal move from Essendon, Little and James Hird.

With 34 past and present Essendon players facing doping bans for part of the 2015 season, Justice Middleton's ruling left Little facing an increasingly divided board concerned at the ongoing damage to the club and the costly nature of his leadership.

Some directors and influential Essendon supporters have also become disenchanted about the return of suspended coach Hird, who also took on ASADA and lost. At least three directors are expected to depart the club before the forthcoming annual general meeting, with one former player and several well-known supporters looking at nominating to achieve a five-four majority over Little and his supporters at the board table.

Justice Middleton not only ruled against Essendon and Hird, and ordering those parties to cover ASADA's legal costs, but also stated he would not have set aside the 34 show-cause notices issued to the players even if he had found the investigation to be unlawful.

The players refused a deal offered by ASADA in June that would have seen them return for round-one next season on the basis ASADA would not put forward its evidence. The majority of Cronulla players in the NRL found guilty of taking banned substances have now served their brief suspensions.

Pointing out that Hird and the players voluntarily took part in the joint interviews, Justice Middleton said: "It can hardly be said Mr Hird and the Essendon players did not consent to the information being disclosed to all in the interview room."

The Bombers hierarchy - confident of victory and indicating recently the club would appeal the decision in the event of a loss - was less bullish after the decision was handed down. While Little has repeatedly stated he did not believe his players had taken banned drugs, on Friday the club mitigated that by saying it believed neither banned nor harmful drugs were administered "on all the evidence available to us".

The finding was a victory for ASADA and specifically its former chief, Aurora Andruska, grilled over her handling of the investigation last month in the Federal Court. While the AFL will shift its focus to preliminary final weekend, Monday night's Brownlow count and the grand final, Justice Middleton's decision was an endorsement of the league's recently maligned process and specifically its integrity officer Brett Clothier and the investigation he ran in conjunction with ASADA.

The feeling from the AFL players' union on Friday was that the footballers were now keen to have the matter resolved. Only one, former Bomber Angus Monfries, now at Port Adelaide, is playing in the preliminary finals. Another, the disillusioned star ruckman Paddy Ryder, will depart the club and could invoke a breach-of-contract clause should Essendon stand in his way.

ASADA's new boss, Ben McDevitt, is expected to move ahead with the show-cause notices.

The anti-doping agency said in a statement on Friday: "The only way to stay ahead of sophisticated doping regimes is to partner with sports; not exclude them from the process ... Our aim has always been to expose what happened at Essendon in 2012 and we steadfastly remain committed to this."