Botting was born in Oakley House near Royal Air Force Station Abingdon (RAF Abingdon) at Frilford Heath near Oxford, England on 19 July 1943. He was christened in the Church of England Parish Church of St. James the Great in Radley, Berkshire. His father, Pilot Officer Norman Arthur Botting DFC, a Dam Buster with 617 Squadron, was killed in action over Germany on 15 September 1943 when Gary was less than two months old—on his older sister Mavis' second birthday. Following the war, their mother Joan, a teacher, took up residence with Group Captain Leonard Cheshire VC, the father of their younger sister, Elizabeth, at Gumley Hall near Bedford Gardens, Market Harborough, Leicestershire and later she and the children moved with Cheshire to LeCourt, the name of the mansion he had acquired from his aunt in Hampshire. After witnessing the bombing of Nagasaki at the end of World War II, Cheshire, who had been raised high Anglican, began to examine various religions. Joan and he agreed about the nature of God as a person. Joan was baptized as a Jehovah's Witness in September 1948 and expected Cheshire to follow; when he converted to Roman Catholicism later that year instead, she moved with the children back to Radley.
Botting attended the Church of England Primary School in Radley. One day when pedaling back from school he found a large sphinx moth, "a rare and portentous Death's-Head Hawk (Acherontia atropos)" at the side of the road. Later, in Cambridge, he began collecting moths in earnest. On Elizabeth's eighth birthday, 8 January 1954, the Botting family arrived in Fort Erie, Ontario as immigrants to Canada.
In his early teens Botting began to experiment at home with the hybridization of moths, developing his own technique entailing surgical transplantation of female pheromonal scent sacs. Exhibits of his hybrid moths won top honours at the Ontario (Canada) and United States National Science Fairs two years in a row—in 1960 for "Interesting Variations of the Cynthia Silk Moth", and in 1961 for "Intergeneric Hybridization Among Giant Silk Moths". In particular, he cross-bred the North American Polyphemus moth (then called Telea polyphemus) with Japanese and Indian giant silk moths of the genus Antheraea, pointing out that the Polyphemus moth really belonged to that genus. The Polyphemus moth was subsequently renamed Antheraea polyphemus to accord with his observations.
In the summer of 1960 he was sponsored by the American Institute of Biological Sciences on a lecture tour of the US to explicate his experiments. Later that year the US National Academy of Sciences sponsored him on a lecture tour of India. While in India in January 1961, Botting was befriended by J. B. S. Haldane, who decades earlier had applied statistical research to the natural selection of moths. In the 1960s, Haldane's wife, Helen Spurway, was also researching the genetics of giant silk moths of the genus Antheraea. Helen Spurway, J.B.S. and Krishna Dronamraju were present at the Oberoi Grand Hotel in Kolkata when 1960 US National Science Fair winner in botany Susan Brown reminded the Haldanes that she and Botting had a previously scheduled event that would prevent them from accepting an invitation to a banquet proposed by J.B.S. and Helen in their honour and scheduled for that evening. After the two students had left the hotel, Haldane went on his much-publicized hunger strike to protest what he regarded as a “U.S. insult." Botting received the US National Pest Control Award when he demonstrated that his experiments had practical applications beyond producing finer silk. In 1964 he experimented with feeding caterpillars juvenile hormones and vitamin B12 to keep Luna moths (Actias luna) and Cecropia moths (Hyalophora cecropia) in the larval stage an instar longer than normal, resulting in larger cocoons and larger adult moths.
Botting was raised as a Jehovah's Witness. At age five, with his sister Mavis (then seven), Botting began going from house to house distributing The Watchtower and Awake!, and the following year gave his first sermon about "Noah and the Ark" at the Cambridgeshire Labour Hall in Cambridge, England. Mavis and Gary attended the semi-official Theodena Kingdom Boarding School in Suffolk, run by Rhoda Ford, the sister of Percy Ford, at that time the head of Jehovah's Witnesses in Great Britain. Botting later documented the harsh discipline by caning meted out to him at the hands of Ms. Ford, who had set up the school in defiance of Thorpeness bylaws; he ran away from school, and contracted double pneumonia. As a result of his mother's intervention, the school was shut down, Ms. Ford was disfellowshipped from Jehovah's Witnesses, and her brother demoted. In 1953, Gary's maternal grandmother Lysbeth Turner, unimpressed by her daughter's choice of religion, attempted to expand Gary's religious horizons by introducing him to Gerald Gardner, the principal advocate of "the old religion" of Wicca to which she adhered.
Botting's lay preaching continued after his arrival in Canada at age ten. He entered the "industrial arts" (rather than "academic") stream in high school, majoring in drafting and machine shop. In July 1955, Botting was baptized as a "dedicated" Jehovah's Witness at a convention in New York City. In July 1961, Watch Tower vice-president F.W. Franz assigned Botting the task of smuggling Watchtowers and anti-Francisco Franco tracts into Spain, where Jehovah's Witnesses were banned. From 1961 to 1963, Botting volunteered in Hong Kong as a "pioneer" missionary, supporting himself by working as a journalist for the South China Morning Post. Once he returned from Hong Kong, he attended Trent University to study literature and philosophy. In 1965, the Peterborough Examiner published a full-page editorial on Botting's personal dilemma, "Evolution and the Bible: Faith in Science or Faith in God a Choice for Man." Botting later admitted that his discussions with Haldane in India in 1961 had had a profound effect on his way of looking at the world, although the process of shaking the social imperatives imposed by his religion took decades.
In 1966, Botting's grandmother visited Canada and once again encouraged him to expand his religious horizons to include "the old religion". This time, she focused her attention on Botting's fiancé, Heather Harden, nominally also a Jehovah's Witness, who was receptive to the idea of establishing a Wiccan coven in Canada. In 1969-70, Gary and Heather Botting established Coven Celeste in Peterborough, Ontario, having by that time become "inactive" Jehovah's Witnesses.