The ultimate purpose of Mary's visit, Elizabeth's counsellors firmly believed to be the dethronement of the English queen and the enthronement of her Scottish cousin.

Elizabeth, in her heart, felt confident that John and his father were not parties to the treasonable plot, although she had been warned against each of them.

Cecil and Sir William St.Loe also secretly held to that opinion, though neither of them expressed it, Elizabeth was conscious of having given to John while at London court an intimation that she would be willing that Mary should visit England.

Of such intimation Cecil and Sir William had no knowledge, though they, together with many persons of the Court, believed that Elizabeth was not entirely averse to Mary's presence.
Lord Rutland and John were questioned by Cecil in the hope of obtaining some hints which might lead to the detection of those concerned in the chief plot, provided such plot existed.

But Lord Rutland knew nothing of the affair except that John had brought the Scottish queen from Scotland, and John persisted in the statement that he had no confederate and that he knew nothing of any plot to place Mary upon the English throne.
John said: "I received from Queen Mary's friends in Scotland letters asking me to meet her on the border, and requesting me to conduct her to my father's castle.