AUGUSTA — Dirigo’s run is over. For now.

The third-seeded Cougars let a nine-point first-half lead slip away Thursday night at Augusta Civic Center. No. 2 Waynflete gradually took control and wiggled away with a 58-51 Western Class C semifinal win.

Gone is a 13-game regional tournament winning streak in this building. For the first time since 2008, there will be a new Western Maine champion after Waynflete and Boothbay collide Saturday night.

“We knew we were playing a tough team tonight and we battled our butts off,” Dirigo coach Travis Magnusson said. “I don’t think a lot of people thought we’d be 18-1 coming into tonight as young as we were. The seniors led this team. They gave us great leadership, and we’re going to be back.”

Dirigo wasn’t done until Travis Frost’s potential game-tying 3-pointer rattled in-and-out with 30 seconds remaining. Riley Robinson’s follow-up also lingered on the rim before taking a Flyers-friendly bounce into the arms of Serge Nyirikamba.

Harry Baker-Connick, Paul Runyambo and Nyirikamba combined to hit four of six free throws in the waning seconds, hoisting Waynflete (19-1) into a regional final for the first time since it faced Oak Grove-Coburn of Vassalboro — a school no longer in existence — in the 1983 Western Class D title game.

“The last 20 seconds, we’re looking at the clock just waiting for it to be all zeroes,” Waynflete senior guard Max Belleau said. “You see (Dirigo) every year, whether they’re beating us or somebody else, they’re definitely there at the end. It feels great to beat that kind of a team.”

Nyirikamba led the Flyers with 17 points. Baker-Connick scored his 12 points all in the second half, including nine in the third quarter, when Waynflete wiped out a 27-23 halftime deficit to take its first lead of the night.

Waynflete was 12-for-17 from the field in the second half while containing Dirigo to 10-of-25 in that span.

“The first half we came out slow. The second half after Coach (Rich Henry) talked to us, we played our game and got more fast break layups,” said Baker-Connick, a sophomore point guard. “They’re a very good team. They’ve won the last four years. After our quarterfinal game practices were more tough, trying to increase to their level.”

Frost finished with 15 points and Robbie Babb 13 in the final game of their Dirigo careers. Tyler Frost added nine points, all on 3-pointers in a first quarter that saw the Cougars explode to a 19-10 lead.

Waynflete held Dirigo freshman Robinson, who erupted for 23 points in a come-from-behind quarterfinal victory over Old Orchard Beach, to two points, seven rebounds and three steals.

“They’re a great team and they made some plays,” Magnusson said. “We got the shots we wanted that went in-and-out, and that was the difference. We played well. When there were (30 seconds) up there, we had a shot go in and out. If we had another (four) minutes, we very well could have won this game. You never know.”

Dirigo scored the first six points of the night and appeared ready to storm into another championship game.

Waynflete turned it over five times and missed eight of its 12 shots in the opening period. Hunter Ross and Travis Frost’s quickness and intensity caused defensive disruptions, as usual, and the Cougars’ calm on the offensive end led to opportunities inside for Babb and outside for Tyler Frost.

“They came out with a lot of intensity and put us on our heels,” Henry said. “We talk a lot about our athleticism. These guys (Dirigo) are very fundamentally sound and they’re scrappy. They were beating us to every loose ball. They were stripping the ball. After a while I guess we settled down.”

The lead was still nine on two free throws by Robinson with 5:42 left in the half, but Baker-Connick found Mohammed Suja for a 3-pointer and Nyirikamba on a drive to the hoop to give the Flyers wings.

Put-backs by Nyirikamba and Joseph Schnier extended the run to 9-1 before an open 3-pointer and a second-chance hoop by Chad Snowman protected Dirigo’s lead at halftime.

“I think we handled adversity a little better. We were a little shaky at first, but we kind of settled down a little bit, especially compared to last year,” Belleau said of a 2012 semifinal loss to OOB. “It was just focusing on taking our time, moving without the ball and getting some open looks, because we forced it a little bit at the start.”

A brief delay after a hard fall by Belleau preceded Waynflete’s go-ahead basket, another Suja 3-pointer that made it 38-36 with 3:19 to go in the third.

Dirigo tied it twice, on a Babb steal leading to a Travis Frost layup, then on a Ross free throw with one second left that knotted it at 42.

Belleau dished down low to Nyirikamba for a deuce in the opening minute of the fourth, and the Flyers never trailed again.

Nyirikamba had eight points in the fourth quarter, when the Flyers missed only one field goal and went 8-for-13 from the line.

“I think we’ve got resilience. These kids have been in big games in soccer. They’ve been here a couple of times, and you really have to get used to it. For Dirigo it’s almost like a birthright for them,” Henry said. “These guys expect to be in the semifinals. That’s what they’re all about. It’s an unbelievable program. It really took a lot of work on our part.”

In the first two years since Magnusson moved over from the defunct Livermore Falls program to Dirigo, the Cougars are 41-3.

“This is a great experience,” Magnusson said. “Maine high school basketball, you can’t beat it, the atmosphere tonight and everything.

And if you have any chance to beat Dirigo with this festive backdrop, at this time of year, by golly, you’d better take advantage.

“I don’t think we could have played worse in the first quarter given the atmosphere and the magnitude of the game, but we bounced back,” Henry said.

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