Elizabeth was in a difficult position …
Mary was a Queen and entitled to be treated like a Queen.
Mary was a Catholic and a possible successor to Elizabeth.
In the 1580s, the Pope declared that it was no sin for a Catholic to murder or be involved in a plot to murder Elizabeth.
So Elizabeth …
Started a tribunal / enquiry into the murder of Darnley. (A queen could not be tried by a court.) The Tribunal did not prove Mary innocent. Neither did it find her guilty. But the “Casket Letters” said to be written from Bothwell to Mary did a lot of damage to Mary’s reputation.
Kept her under guard in a series of castles. She was moved from the North. (Too close to Scotland and too many English Catholics) to the midlands of England.
