Historians believed the flightless creature had been kept alive in a 17th Century London townhouse.
But recent forensic analysis of its skull found lead shot pellets, which were typically used to hunt wildfowl.
Scientists hope to test the fragments to establish where the bird met its end.
Oxford University has held the mummified skull and foot at its Natural History Museum for more than 300 years.
The specimen represents the most complete remains of a single dodo, and contains the only soft tissue samples known to exist.
It has proved invaluable in learning more about the species, which became extinct 70 years after it was discovered on the island of Mauritius in 1598.
But the Oxford Dodo's own fate had remained a mystery.
However, a team at the University of Warwick used forensic CT scanning to create a three-dimensional digital replica of its skull.
The technology, which has also been used in criminal trials, showed evidence that the bird had been shot in the back of the head and neck.
Prof Mark Williams, of the university's Warwick Manufacturing Group, said:
When we were first asked to scan the Dodo, we were hoping to study its anatomy and shed some new light on how it existed. In our wildest dreams, we never expected to find what we did.