Imprisoned WikiLeaks whistleblower Chelsea Manning filed an appeal this week, three years after she was sentenced to 35 years in prison for what is still considered the largest leak of classified government documents in history.

Manning, a former Army intelligence analyst who was known as Bradley Manning at the time she was prosecuted, was sentenced in a military court in August 2013 for leaking about half a million classified documents to the secret-spilling WikiLeaks site in 2010. Her attorneys have asked a military appellate court to dismiss her case or reduce her sentence to 10 years, which was the original sentence she sought at the time of her court-martial trial.

Manning’s attorneys waited to file her appeal to the US Army Court of Criminal Appeals until yesterday, the deadline for submitting. So what took them so long to file?

Shortly after sentencing in 2013, Manning’s trial attorney, David E. Coombs, had sought clemency for his client from the Army—a process that took months to conclude. The military rejected the request in April 2014, at which point the case was automatically referred to the appellate court.

But this wasn’t the primary reason for the delay. The unprecedented case posed a number of difficulties for Manning’s defense attorneys, says Vincent Ward, co-counsel for the Chelsea Manning Legal Defense team. This extended the time it took to prepare an appeals brief. The case not only involved enormously complicated legal and technical issues, he says, but also involved a mix of classified and unclassified information that was logistically difficult and time-consuming for defense attorneys.

“There aren’t a lot of classified-and-unclassified trials,” Ward says. “It’s one thing to look at the unclassified portion [of court records], which is itself enormous, but it’s something entirely different to go through the classified portion, [which] is very administratively burdensome.”

It took the government many months to produce the full trial record for Manning’s defense team to review. Although the attorneys received a shipment of unclassified documents, the classified documents remained at Ft. Belvoir, Virginia, where the appeals court resides. Attorneys could only examine the documents in a SCIF—a highly secured Sensitive Compartmented Information Facility—and they could only discuss the classified information contained in those documents in the SCIF, too.

This was further complicated by the fact that some hearings in the case involved both classified and unclassified information in the same session, which meant that transcripts and records for a single hearing would be in different locations. “You may be reading about something that’s unclassified, and in order to complete it you have to look at the classified portion,” Ward says.

Discussing that classified information with their client—who is currently incarcerated at Ft. Leavenworth in Kansas—presented additional hurdles. “[I]t’s not like I can shoot her an email,” Ward says.

These were just the difficulties involved with the classified documents. But Ward says the volume of unclassified documents they had to review also presented problems. “You’re talking about like 90 volumes of unclassified material, of 500 pages each in a volume. And it’s not like it’s organized very well when you get it.” He says it took his staff three months just to organize the records in a manner that made them useful. And once they wrote the 200-page appeals brief, the government had to review it to make sure it didn’t expose classified information.

Ward says the appeals process, and the initial trial, were also made more difficult by how the government handled the case.

“The government was ridiculous in its prosecution strategy. It over-complicated the case,” he says. This was due in part to the government’s aggressive stance in prosecuting whistleblowers in general and Manning in particular, and to the fact that Manning was a soldier and was being tried in a military court.

“This was by far one of the most complicated cases that the Army is ever going to deal with,” Ward says. “They’re not the Department of Justice. They don’t have loads of lawyers waiting to work on complicated [espionage] cases.”

He also says the military prosecutors complicated the case needlessly by over-charging Manning. Manning was initially charged with more than 22 counts, including aiding the enemy, a capital offense that potentially carried a death sentence—although the government asserted that it never planned to pursue a death sentence. The case also involved numerous technical details as well as last-minute evidence that prosecutors introduced during its closing arguments in the case.

Manning pleaded guilty to a subset of the charges involving mishandling of classified documents. She was then acquitted on the aiding the enemy charge but was found guilty of 19 other counts, including five counts for violating the Espionage Act, five counts of theft, and one count of unauthorized computer access.

When it came time for sentencing, Ward says the complex nature of the case overwhelmed the military judge, and this is reflected in the sentence Manning got. The government had asked for 60 years, but Manning’s attorney sought 10 years. “And the judge picked a mid-point because she had no frame of reference on how to sentence Chelsea. All of those [complicated] factors contributed to Chelsea getting a historically outrageous sentence.”

The sentence was unprecedented for a leak case.

“Manning is one of very few people ever charged under the Espionage Act prosecutions for leaks to the media,” Elizabeth Goitein, co-director of the Liberty and National Security Program at the Brennan Center for Justice at New York University Law School told WIRED at the time of Manning’s conviction. “The only other person who was convicted after trial was pardoned. Despite the lack of any evidence that he intended any harm to the United States, Manning faces decades in prison. That’s a very scary precedent.”

The American Civil Liberties Union, the Electronic Frontier Foundation, and other civil liberties groups have filed amici briefs in support of Manning’s appeal, arguing that Espionage Act prosecutions for disclosures of information to the press are unconstitutional under the First Amendment.

There won’t be any resolution of the appeal soon, however. The government will need time to file its brief, after which the court will set a hearing for oral arguments. And before the appeals court can make any decision on Manning’s request, it will also need to re-review the trial records.

Unlike federal appellate courts that review very narrow legal aspects of a case and send a case back to a trial judge to re-sentence a defendant if the appeals court finds that the trial court or prosecutors handled a legal issue improperly, the military appellate court has much more authority, Ward says.

“There’s really no federal equivalent to it,” he says. “[The military appeals court] gets to sit in the seat of the trial judge and do virtually everything all over again, including re-sentencing Chelsea if that’s what it chooses to do.”

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Chelsea Manning’s Appeal Took Three Years to File. Here’s Why