This was the time of Titus Oates and the "Popish Plot", and some of Walker's writings made him a suspect; however, no serious steps were taken against him, although Oxford booksellers were forbidden to sell his book, The benefits of our Saviour Jesus Christ to mankind.

In spite of growing unpopularity, he remained loyal to James, and when the king fled from England, Walker left Oxford, doubtless intending to join his master abroad.

But in December 1688, he was arrested at Sittingbourne and was imprisoned; then, having lost his mastership, he was charged at the bar of the House of Commons with changing his religion and with other offences.

Early in 1690, he was released from his confinement, and spent his last years subsisting largely on the charity of his friend and former pupil at University College, Dr John Radcliffe.

[4] Walker was responsible for the statue of King James II on the tower in the main quad at University College, one of only two in England.