outh ice-hockey team The Mighty Ducks and their captain Charlie Conway are awarded the junior varsity hockey scholarships to Eden Hall Academy, a prestigious Minneapolis-area prep school that Coach Bombay attended. Charlie struggles with his transition from childhood to adolescence; he thinks he was abandoned by Bombay when the latter informs him that he intends to take a job with the Junior Goodwill Games, which would leave him unable to coach the Ducks; one of the Ducks' enforcers, Dean Portman, also decided not to attend the school after hearing about Bombay's leaving and Jesse Hall also does not attend. Bombay informs Charlie prior to the start of classes that the team will be in good hands under the tutelage of coach Ted Orion, a former NHL player.
The Ducks' start at the school begins inauspiciously; while the newer Ducks respectfully sit in at the headmaster's speech, the original teammates crash the ceremony on stage. The team then experience many early struggles: playing in the new "two-way hockey" defensive style of Coach Orion, Orion abandoning several Duck traditions and some of their youthful in-game 'trick' plays, and off-ice conflicts with the Varsity team. The Ducks' struggles continue, culminating in a tie in their first game after having a huge lead. Eventually, when Coach Orion restricts the old Ducks uniform after an unsanctioned early morning match with the Varsity team to settle their differences, Charlie decides to leave the team to return to public schools and seek a hockey career. Fulton follows, but considers quitting hockey much to Charlie's dismay. Sometime later, he ultimately returns to the team without Charlie.
Angry at Bombay's departure and at Orion's highly disciplined coaching style, Charlie's acting out alienates him from his mother, Hans (Gordon's old mentor and friend of the Ducks), and even his friends. Hans suddenly dies, and Bombay comes to Charlie's house the day following the funeral and takes him back to Eden Hall. He tells Charlie that Orion's career with the Minnesota North Stars ended when the team moved to Dallas and he stayed to care for his paraplegic daughter. Bombay tells Charlie the background story on how he first came to coach the Ducks and says he told Orion that Charlie was the heart and soul of the team, and it was his hope that both Orion and Charlie would learn something from each other. Bombay also admits telling Orion that Charlie was the real "Minnesota Miracle" man. Emotionally touched by his words, Charlie agrees to rejoin the team.
Arriving at the team bus for the next game, Charlie tells Orion he wants to play "two-way hockey". Surprised but pleased, Coach Orion welcomes him back. Before they depart, Dean Buckley, the school's headmaster, informs the team that its board of trustees wants to revoke the Ducks' scholarships and offers Orion a chance to start anew with a team of his choice. Satisfied with the team, Coach Orion balks at the news, threatening resignation. At a board meeting the following day, Bombay, who was an experienced lawyer before coaching the Ducks, acts as the Ducks' attorney and fights successfully for their case, and the board reinstates the Duck's scholarships.
Prior to the annual JV–Varsity game, Orion brings back the Duck jerseys, giving the team a renewed vigor. Throughout the game, the Varsity dominates on offense. However, the Ducks play good defense and manage to keep the game scoreless after two periods. During the second intermission, Dean Portman returns to the team (having finally accepted his scholarship), adding a needed spark. Late in the game, the Ducks get two penalties and must play 5 vs 3. During the time-out, Orion reinstates Charlie as captain and tells him to go for the win if the opportunity presents itself. With seconds left in the game, Charlie gets a breakaway and beats all the defensemen and goalie; he passes the puck back to Goldberg, now a defenseman, who scores into an wide-open net as time expires, securing a 1–0 victory for the Ducks.
Following the victory, Charlie embraces Orion and spots Bombay who has attended the game, and they both look across the rink to a newly-presented Eden Hall banner with the Ducks' logo. Bombay then departs the game amid a sea of cheering fans, with a smile.
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