HOOVER, Ala. — It wasn’t supposed to end this way.

If Georgetown’s entire season taught us anything, it was that senior centerback Tommy Muller’s 89th-minute header in Sunday’s national championship against Indiana (15-5-3) was destined for the top-right corner and the back of the net.

But then the crossbar rang out — and with it rang the realization that the historic 2012 Hoyas’ late-game magic had finally run out. The Blue and Gray (20-3-3) had won 16 one-goal games this season and had mounted gutsy second-half comebacks against both Syracuse and San Diego in the earlier rounds of the NCAA tournament, but Sunday wouldn’t see a repeat performance: Playing for the first title in program history, they came up just short in a 1-0 loss.

After first congratulating Indiana in his postgame press conference opening statement, Head Coach Brian Wiese continued, “I also have to say … that it’s a real honor and privilege to represent Georgetown University, this athletic department and this student body. Seeing how this team galvanized the Georgetown community was inspiring for everybody. It hurts as much for these guys as it does for all of Georgetown that we weren’t able to come out with a national championship today.”

That pain was visible in the players and staff after the final whistle blew, as a number of Hoyas remained on the ground in disbelief minutes after the game had ended. A runner-up trophy — which Wiese called “one of the sourest things you can look at” in the immediate wake of the loss — and a College Cup Most Outstanding Offensive Player award for junior forward Steve Neumann were of little consolation.

The first half showed some warning signs, as through-balls and lofted passes over the top troubled the Blue and Gray backline right from the get-go. Sophomore forward Eriq Zavaleta was a handful for Muller and the rest of the Georgetown defense all afternoon, but the highly touted MLS prospect was limited almost exclusively to tough-angle looks in the opening 45.

Sophomore midfielder Tyler Rudy got the Hoyas’ best look of the half in the first 10 minutes, teeing up an open look from inside the box toward the right corner that was acrobatically saved. The Hoosiers looked the better side other than that, however, and Georgetown’s two uncharacteristic subs in the closing minutes further hinted at lingering fatigue from Friday’s marathon win over Maryland.

“It’s tough when you do a Friday-Sunday format and have these types of games,” Wiese affirmed. “With the pressure of it as well, it’s hard to get those legs turned over. Indiana played a hard game on Friday as well, so they maybe did a better job getting their legs back under them.”

For a Georgetown squad running on fumes, then, getting the first goal was essential. It didn’t happen.

After a couple fruitless corner kicks out of the locker room, Indiana struck in the 64th minute. Sophomore goalkeeper Tomas Gomez — who put in a strong performance in the first half — found himself caught in no-man’s land on a cross to the back post, leaving his line but not getting to the ball in time to beat Zavaleta to it. The Hoosier star headed it over to wide-open teammate Nikita Kotlov, and the junior midfielder made no mistake with the empty net that lay before him.

Still, with their trademark flair for the dramatic in mind, Muller noted that Indiana’s goal did nothing to detract from his team’s self-belief.

“Throughout the season, we’ve always trusted our style and how we play,” he said. “In this game, we believed we were going to score the whole time. We had some chances to put a goal away. Indiana made it really tough. They played a fantastic game.”

Muller was responsible for two of Georgetown’s major chances, the first coming off of a Neumann corner in the 78th minute and the second his effort that ricocheted off the woodwork in the dying moments.

“We just kept pressing. We didn’t really change our mentality until [there were] two minutes left and we started just putting stuff in the box,” senior central midfielder Ian Christianson said. “I think the guys played their hearts out today.”

The Hoyas — who lit up the scoreboard with four goals Friday against the Terps — were shut out for just the second time this season; the only other instance came in South Bend against Notre Dame, whom Indiana eliminated in the second round.

Nonetheless, Sunday’s loss should not mask the fact that 2012 marked what was by far the best season in program history. Muller and Christianson both played huge roles in their team’s turnaround over the course of their four years on the Hilltop, having gone just 9-8-2 in their rookie campaign before reaching the second round of the NCAAs as sophomores. A tourney-less 2011, though, allowed the Hoyas to subsequently fly under the radar, starting off unranked before an opening win over Virginia propelled them into the Top 25.

And as this season wore on, it gradually became apparent that this edition of the Blue and Gray might be something special. A run to the Big East tournament final confirmed it, and the victory over Maryland suggested that ‘special’ very well might mean a title.

“[The program] is night and day since we were freshmen,” Muller said. “The whole mentality of our team has changed, and that has a lot to do with our leadership of the senior class, the coaching staff and the talent we brought in. Every player on our team wants to be a pro.”

The revolutionary graduating class of Muller, Christianson, Nealis and Riemer will all surely get those shots at professional soccer in the months to come.

For the rest of the Hoyas, 90 lost minutes at Regions Park on Sunday left them as one of 202 Division I teams once again left looking toward next year.