The English Civil Wars were a pair of armed conflicts between the forces of Parliament and King Charles I in the mid seventeenth century. Oxford played a pivotal role in the first war.
Despite (marginal) success at Edgehill and a conclusive victory at Brentford, in November 1642 Royalist forces met a much stronger Parliamentary army at Turnham Green. The King had no option but to retreat to Oxford, which became the Royalist capital of England for the remainder of the war.
The University took the Royalist side throughout the hostilities, and provided Charles and his retinue with facilities and accommodation. The view among the townsfolk was not so clear cut: some of them found it expedient to flee the city.
In 1645, however, the war turned decisively against the King: Fairfax's New Model Army crushed Royalist forces at Naseby and then Langport. Charles fled Oxford, eventually disbanding his army and finding refuge with the Scots. In 1646 he was delivered to parliamentary custody, bringing an end to the First Civil War.
More information on the Civil War in relation to Oxford is available from the County Council at http://www.oxfordshire.gov.uk/index/libraries_heritage_countryside/oxfordshire_museums_service/virtualexhibitions/storyofoxford/civil_war.htm.