The investigation came to a dramatic head late on Tuesday when stone-faced administrators slapped the Melbourne team with the harshest punishment in the Australian Football League's (AFL) 116-years, for using their players as guinea pigs in an experimental and possibly illegal supplements regime in 2011-12.
One of the nation's oldest and most successful AFL clubs, with a record of 16 championships equalled only by cross-town rivals Carlton, Essendon's 2013 season ends in ignominy, disqualified from competing in the playoffs next month and hit with a A$2 million ($1.79 million) fine.
The club, which declared more than A$65 million in revenue last year, has also been stripped of draft picks for the next two seasons, while head coach James Hird, a former champion player and one of the game's most revered identities, has been banned for 12 months.
Rival clubs and players in the popular 18-team league hope the stinging punishment will put a line under a scandal which has tainted the innocent along with the guilty and reduced the on-field action to a sideshow.
But the sprawling investigation launched by the Australian Sports Anti-doping Authority (ASADA) in February, dubbed "the blackest day" in sports history Down Under by a former chief of the agency, continues.
Attention will now turn to punishments for individual players, which could see offenders banned for two years.
"There is no evidence at the moment to issue infraction notices to players about the use of prohibitive substances," AFL chief Andrew Demetriou told reporters.
"ASADA has made it clear they have an ongoing investigation, so that part of it remains open."
At the heart of the scandal are the use of peptides, small chains of amino acids that can be taken in supplement form to aid in muscle growth and re-generation. A number of peptide hormones have been banned by the World Anti-Doping Agency.
Stephen Dank, a sports scientist who helped Essendon source supplements and set up their programme, denied giving players banned drugs in an interview with state broadcaster ABC earlier this year.
But Dank's work as a consultant at Cronulla Sharks in 2011 has made the National Rugby League team another target in ASADA's investigation.
Investigators will also probe AFL team Melbourne Demons, Demetriou said. Melbourne's club doctor Dan Bates was stood down in April amid an internal review into supplements use after revelations that he had consulted with Dank.
Essendon's captain Jobe Watson, who won the AFL's most valuable player award last year, made a stunning admission on a local television chatshow in June that he believed he had taken AOD-9604, a banned anti-obesity drug.
An independent review commissioned by Essendon earlier this year found a "disturbing picture of a pharmacologically experimental environment" at the club.
The AFL's charges alleged Essendon had sourced and administered banned substances to players, had failed to check with anti-doping authorities as to their legality or adequately recorded details of their supplements programme.
Essendon have denied they are drug cheats, however, and only conceded after two days of legal wrangling with the AFL there was a "risk" they could have administered banned substances to players and were "unable" to determine whether they had.
The club's gradual but inexorable downfall has captivated Australia's AFL-obsessed southern states for months, and its punishment knocked the federal election campaign off the front pages of Wednesday's newspapers across the country.
"Bombed" shouted the front page headline of Sydney tabloid, the Daily Telegraph, with the back page headlined "Essendone."
The Australian newspaper's banner was: "Final humiliation for Essendon".
Prominent AFL columnist Patrick Smith described Essendon's failure to look after its players' welfare in 2012 as "the darkest year in AFL history."
"It is what we pray to God did not happen at any other clubs in the AFL," he wrote in The Australian.
Head coach Hird, who had long denied any wrongdoing and launched legal proceedings against the AFL last week, accepted the ban on Wednesday and dropped the legal action, saying it was "time to move on".
He also apologised for his role in the scandal, but remained defiant he had not broken any rules.
"Not at all," he told reporters on Wednesday outside his home in Toorak, an affluent suburb of Melbourne.
"I didn't break the rules ... those charges have been dropped. We've agreed to move on."
($1 = 1.1154 Australian dollars)