Police used DNA to identify the torso, and said it had been mutilated and bound to heavy metal in an apparent attempt to sink it, according to the BBC.
“It is with boundless sorrow and dismay that we received the news that the remains of our daughter and sister Kim Wall have been found,” Ingrid Wall wrote on Facebook Wednesday — nearly two weeks after her daughter disappeared and her case gripped the world.
“It began with a crazy scientist who we thought was a victim, as his submarine disappeared accidentally with a Swedish journalist onboard,” the editor of Denmark's largest daily newspaper told The New York Times.
“Our emotions were completely turned around as he went from victim to possible perpetrator.”
Wall was last seen on the evening of Aug. 10, leaving the Copenhagen harbor with Madsen in the Nautilus — which is described on its website as “one of the world's largest home-built submarines.”
The reporter's family said she was working on an article about Madsen, 46. He built the Nautilus nearly a decade ago, and has since launched plans to build a crowdfunded space laboratory, according to the BBC.
After reporting from the heart of postwar Sri Lanka and the capital of North Korea, taking a submarine trip with a passionate inventor seemed typical for the 30-year-old reporter, as her friends told it.
“That was what she did. She just wandered places,” said Christopher Harress, a reporter for AL.com, who met Wall when they both studied at Columbia University.
“She trusted somebody, and then this is what happened,” Harress told The Washington Post.
Wall was supposed to return from the Nautilus that evening. Police began to search the next morning, after boyfriend reported her missing.
The same morning, the Guardian reported, Madsen was spotted leaping from the Nautilus into a bay as the submarine began to sink.
He was rescued, and first told police that he dropped Wall off at the harbor the previous evening, as planned — and had barely escaped his ship after the ballast tank malfunctioned.
But a witness contradicted this. He told reporters that he saw Madsen go down into the belly of the vessel, then calmly emerge and stay in the submarine's tower until water began pouring into it.
Only then did Madsen swim to a nearby boat, the witness said.
Copenhagen police arrested Madsen on a charge of involuntary manslaughter after the sinking, according to a police news release, and accused him of deliberately wrecking the submarine.
Investigators found blood in the vessel when they lifted it from the bottom of the bay, according to the Associated Press.
“There is nobody on board — neither dead nor alive,” Copenhagen's homicide chief told reporters at the time, and claimed the vessel had been intentionally sunk.
Madsen was arrested and charged with involuntary manslaughter, and ordered to he be held for 24 days while police investigated.
He denied the charge, but his story has since changed almost entirely, according to police.
On Monday, investigators announced that he'd admitted Wall died on board and he disposed of her body — though a police statement did not specify what "accident" Madsen claimed killed her, or explain how the submarine sank.
That same day, according to CNN, a cyclist found a female body — armless, legless and headless -- washed up on a shore near the submarine's route.
The body “washed ashore after having been at sea for a while,” Copenhagen police investigator Jens Moeller Jenson told reporters, according to the AP.
Police were able to match DNA from the torso to Wall’s toothbrush and hairbrush, along with blood in the submarine.
The cause of the journalist's death is not yet known.
Cleve R. Wootson Jr. contributed to this post, which has been updated.