(CNN) The pharmaceutical company responsible for one of the largest drug price increases in US history "knowingly paid illegal kickbacks" as part of an elaborate scheme to make millions and stick the American taxpayer with the bill, the US Department of Justice said Wednesday in a lawsuit filed against Mallinckrodt Pharmaceuticals.

In its complaint, the government demanded a jury trial that would put front and center the actions of the company at the heart of a 97,000% drug price hike. The price of Mallinckrodt's anti-inflammatory drug Acthar -- best known for treating babies with a debilitating seizure disorder -- has gone from $40 a vial in 2000 to nearly $39,000 today.

The complaint was filed in the US District Court for the Eastern District of Pennsylvania by US Attorney William McSwain. Mallinckrodt could face fines of nearly $240 million if found liable.

The government alleged Mallinckrodt used a foundation, called the Chronic Disease Fund, as a conduit to pay kickbacks as part of the scheme to maintain the high price of Acthar.

"The scheme allowed the Company to continually raise Acthar's price yet market it as 'free' to patients and doctors, shifting the drug's ever-increasing cost to Medicare," the government said in its complaint. "As a result of its conduct, Mallinckrodt caused the submission of millions of dollars in false Medicare claims for Acthar."

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