The film opens with team captain Charlie Conway (Joshua Jackson) and his teammates being awarded junior varsity hockey scholarships to Eden Hall Academy, a prestigious prep school that Bombay attended. The Ducks experience many early struggles: playing in the new defensive style of coach and former NHL player Ted Orion (Jeffrey Nordling), Orion abandoning several Duck traditions, and off-ice conflicts with the Varsity team, culminating in a tie in an exhibition game, after having a huge lead. Eventually, when Coach Orion restricts the old Ducks uniform, Charlie decides to leave the team. Fulton follows, but returns.
Throughout all this is a subplot dealing with Charlie's transition from childhood to adolescence, as he struggles with what he perceives as abandonment 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. He informs Charlie prior to the start of classes that the team will be in good hands under Coach Orion's tutelage. Angry at Bombay's departure and at Orion's highly disciplined coaching style, Charlie's acting out alienates him from his mother, Hans, and even his friends.
The Ducks' struggles appear to continue as their mentor, Hans, passes away. Bombay comes to his house the day following the funeral and takes Charlie 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 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. 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. Prior to the bus' departure, Dean Buckley (David Selby), the school's headmaster, informs the team that its board of trustees wants 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. He gets Bombay to fight for their case, which he does successfully. Varsity still wants the Ducks out of their school. They been bullying them the entire hockey season to get them to leave. This time will settle this war for good in the JV-Varsity game. The Ducks made a bet if Varsity wins, they will leave Eden Hall Academy. If the Ducks win, they will change Warriors into Mighty Ducks as the new mascot of Eden Hall Academy.
Prior to the JV-Varsity game, Orion brings back the Duck jerseys. 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, adding a needed spark. Late in the game, the Ducks get two penalties and must play 5 vs 3. During the time-out, Orion renames Charlie captain and tells him to go for the win if the opportunity presents itself. With seconds left in the game, Charlie 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. Varsity exits the ice with being humiliated and defeated by the Ducks for good.
Following the victory, Charlie embraces Orion and spots Bombay who has attended the game, and they both look across to a banner with the Ducks' logo. Bombay, then departs the game, amid a sea of cheering fans, with a smile.
- Emilio Estevez as Gordon Bombay
- Joshua Jackson as Charlie Conway
- Jeffrey Nordling as Coach Ted Orion
- David Selby as Dean Buckley
- Heidi Kling as Casey Conway
- Joss Ackland as Hans
- Elden Henson as Fulton Reed
- Shaun Weiss as Greg "Goldie" Goldberg
- Vincent Larusso as Adam Banks
- Matt Doherty as Lester Averman
- Garette Ratliff Henson as Guy Germaine
- Marguerite Moreau as Connie Moreau
- Michael Cudlitz as Cole
- Christopher Orr as Rick Riley
- Aaron Lohr as Dean Portman
- Colombe Jacobsen as Julie Gaffney
- Kenan Thompson as Russ Tyler
- Mike Vitar as Luis Mendoza
- Ty O'Neal as Dwayne Robertson
The film was poorly received by critics. It holds a 20% of positive ratings at Rotten Tomatoes. John Anderson, from the Los Angeles Times, called the film "a self-reverential salute to Ducks" while also saying that the film was "lazier" than its predecessor.
The movie debuted at No.4 in the box office and ended up grossing $22,936,273 in the US. It is the lowest grossing film of the trilogy.