The freelance journalist wrote for leading magazines and newspapers, and was last seen waving to her boyfriend as the vessel sailed off into the Baltic.
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Wall's dismembered torso was found off the coast of Copenhagen later that month, and other body parts were also discovered in the sea in plastic bags in October.
Judge Anette Burkoe at the Copenhagen City Court said she and the two jurors agreed Wall's death was a murder, saying Madsen didn't given "a trustworthy" explanation. Madsen was also found guilty of sexual assault and the defilement of a corpse. In Denmark, a life sentence equates to 16 years, but can be extended if necessary.
Madsen stood quietly listening as the judge read out the verdict Wednesday.
"We are talking about a cynical and planned sexual assault and brutal murder of a random woman, who in connection with her journalistic work had accepted an offer to go sailing in the defendant's submarine," Burkoe told the court.
Madsen, 47, denied murder and said Wall died accidentally inside the submarine, but confessed to cutting up her body and throwing the body parts into the sea. He had changed his story several times following Wall's disappearance.
Initially he told authorities that he had dropped her off on shore and did not know what had happened to her. He then claimed she had died accidentally when hit in the head by the submarine's hatch. Finally, after her decapitated head was found by police divers in a weighted-down bag along with her appendages and the skull showed no signs of fracture, he said she had been asphyxiated in a malfunction aboard the submarine.
The cause of death has never been established but the court found that Madsen "cut the body into pieces to hide what had happened."
Prosecutor Jakob Buch-Jepsen argued Wall's murder was sexually motivated and premeditated because Madsen brought along tools he normally didn't take when sailing.
Madsen plans to appeal, his lawyer Betina Hald Engmark said. He will remain behind bars during that process.