During a consultation with Elizabeth he advised her to seize Mary, should she enter England, and to check the plots made in Mary's behalf by executing the principal friends of the Scottish queen.

He insistently demanded that Elizabeth should keep Mary under lock and key, should she be so fortunate as to obtain possession of her person, and that the men who were instrumental in bringing her into England should be arraigned for high treason.
John certainly had been instrumental in bringing her into England, and if Cecil's advice were taken by the queen, John's head would pay the forfeit for his chivalric help to Mary.
Elizabeth was loath to act on this advice, but Cecil worked upon her fears and jealousies until her mind and her heart were in accord, and she gave secret orders that his advice should be carried out.

Troops were sent to the Scottish border to watch for the coming of the fugitive queen.

But Mary was already ensconced, safely, as she thought, in Rutland Castle under the assumed name of Lady Blanche.

Her presence at Rutland was, of course, guarded as a great secret.
Dorothy's mind dwelt frequently upon the fact that John and the beautiful young Scottish queen lived under the same roof, for John had written to Dorothy immediately after his return.