In 1995, Rutherford replaced Sir Richard Stevenson as minister. He saw himself as a more modern man than Sir Richard and, unlike him, believed that P.R.o.B.e. was called out far too rarely to be worth continued funding. He transferred Louise Bayliss whilst Liz Shaw was taking compassionate leave following her father's death as his first step to closing it down.
When Liz returned to duty, Rutherford had D.I. Burke summon Liz to Whitehall, where he informed her that she would have to prove P.R.o.B.e.'s usefulness in the days to come in order to ensure its continued existence. He was unable to shut the organisation down without Patsy Haggard's agreement and attempted to get her to agree with him by subtly threatening her career progress. She wrote a report on the events at Winterborne School which persuaded him to keep P.R.o.B.e. alive. (HOMEVID: The Devil of Winterborne)
Some time later, Liz and Colonel Ackroyd were tasked with investigating BEAGLE. However, to protect Julius Quilter, Rutherford would not give them proper access nor supply Ackroyd with more men. Eventually, he went with Patsy and Liz to question him, where they met Emerson. After Quilter's death, he gave the BEAGLE file to Emerson, who planned to kill him. He was saved by Liz and Ackroyd.