He established the Canada men's national ice hockey team program in September 1963, seeking players with athletic and academic morals committed to their studies and training.

[12] Bauer aspired to play in the National Hockey League (NHL) and attended training camp for the Boston Bruins held in Hershey, Pennsylvania in October 1941.

[15] Bauer played one final game for the Majors in the 1944–45 season, shortly before he enlisted in the Canadian Army on November 24, 1944, and assigned to Basic Training Unit 12 in Chatham, Ontario.

[30] He and the Basilian fathers lobbied for a shortened schedule for the Toronto St. Michael's Majors in the OHA's top tier of junior hockey after the 1958–59 season, since they believed it was too long and detrimental to academic studies for their students.

[40] UBC physical education teacher Bob Hindmarch became general manager of the Thunderbirds and made the financial and academic arrangements for the players to get to Vancouver.

The Thunderbirds combined with players from the Toronto Marlboros to play an exhibition game versus the Soviet Union national ice hockey team, but lost by a 6–0 score.

The Thunderbirds reached the final game of the Canadian Interuniversity Athletic Union men's ice hockey championship tournament in Kingston, Ontario.

[49] Bauer spoke with American coaches during the World Championships, and learned of their detailed preparation plans for the 1964 Winter Olympics, whereas Canada did not yet know which team would represent the country.

[50] Bauer suggested it might be time for Canadian universities and colleges to represent the country since they met amateur eligibility requirements, and he felt there were young men who would be interested in a program which combined education and hockey.

[54] When the CAHA approved the plan with only 20 minutes of discussion, journalist Trent Frayne stated that "Father Bauer is the greatest lobbyist in the history of hockey".

[60][63] Most of the team lived on the Point Grey campus of the University of British Columbia in a house which had previously been a transmitter station during World War II.

Bauer recruited a German housekeeper named Ma Byers from a local restaurant in Vancouver to cook and act as a mother figure to the players.

[66] Bauer's national team played its first game wearing Canadian jerseys on November 12, 1963, in an exhibition win versus the Melville Millionaires.

[14][69][71] The national team played an exhibition tour in Europe after the Olympics then had an audience with Pope Paul VI in the Vatican City on February 15, 1964.

[74] At the CAHA general meeting in May 1964, Ahearne clarified that the decision to place Canada fourth in the standings was supported by the IIHF statutes and that no rules were changed.

He attracted a following as a priest in Europe, and conducted mass at various locations including motels with a portable altar, a chapel within the Embassy of France in Moscow, churches in Prague and houses of his friends.

[78] Bauer conferred with CAHA president Lionel Fleury, and discussed the merits of skipping the next World Championships to regroup and give the players more time to develop as a team.

[81] At the 1966 Ice Hockey World Championships, Bauer expressed his frustrations about officiating at international events after a loss to Czechoslovakia by a 2–1 score, which saw two Canadian goals disallowed.

[84] At the 1967 Ice Hockey World Championships, Bauer's team won four of seven games played, but lost to the Soviet Union by a 2–1 score and finished with the bronze medal.

Bauer was appointed a member of the board of directors, which decided at its first meeting to make the eligibility of professionals at the World Championships its priority for improving the national team.

[88] His participation in the national team ended in 1969, when Canada was granted permission by the IIHF to use a limited number of professionals while hosting the 1970 Ice Hockey World Championships.

[14] He offered advice to Tom Watt on selecting a Canadian team for the 1972 Winter Universiade, but chose not to coach or manage since Canada had not yet returned to international play.

[91] Bauer wrote an article published in the Toronto Sun on September 2, 1972, giving reasons why he expected total victory in the 1972 Summit Series featuring Canada's top professional players.

[85] He was interviewed on television by Bill Good during game three on the series, and stated that the losses were indicative of domestic hockey issues in Canada, and that we could learn from the Soviets instead of underrating their abilities.

The team finished in fifth place with two wins and five losses and avoided relegation to Group C.[88][95] The CAHA agreed to return to international play as of the 1977 Ice Hockey World Championships when professionals were allowed to participate.

[99] After the Olympics, Bauer gave an interview with The Globe and Mail and made no excuses for the sixth-place finish, but felt that the establishment of a permanent national team had been completed.

A relationship for clinics run by UBC instructors had been developed by Bob Hindmarch, but Bauer was unable to travel since he was infected with shingles at the time and recommended another coach instead.

[3][102] Bauer was an advocate for players remaining in amateur hockey to receive an education, as opposed to the growing professionalism in the being detrimental to opportunities from learning.

[8] He felt that hockey was a means to teach the game of life and way for boys to become men, and modelled the national team after his experiences at St. Michael's.

[14][37][88] Funds from the sale of the Bauer's family cottage were donated to endow the Quest Program to assist in communicating faith by electronic means at the Athol Murray College of Notre Dame in Wilcox, Saskatchewan.