Atsushi Nomi walked through Union Square alongside teammate Takashi Toritani, heading south on San Francisco’s Powell Street in the direction of Samurai Japan’s hotel, a little after midnight Monday morning, just hours after Japan was eliminated from the World Baseball Classic.

The square was lit by the soft glow of street lamps and the light that emanated from the concentration of upscale establishments populating this part of The City by the Bay’s downtown area, but with everything long since closed for the night, there was nowhere for the Hanshin Tigers duo to go.

AT&T Park would also be bright, yet tantalizingly off-limits hours later, when the World Baseball Classic kicked back into high-gear. Because for the first time, Nomi and Japan had no where to go and no more games to play. Japan lost to Puerto Rico 3-1 in the WBC semifinals on Sunday, and were in the air, headed home and back to their various teams, by the time the tournament resumed Monday night.

Past managers Sadaharu Oh and Tatsunori Hara guided Japan to titles in 2006 and 2009, but whether or not Yamamoto followed in their footsteps in 2013, Japan’s reign was going to end sooner or later.

Still, the ending was a bitter pill to swallow Sunday, when a weak offensive effort allowed the Puerto Rican pitchers to nurture an early one-run advantage long enough for Nomi to hang a change-up that Chicago White Sox outfielder Alex Rios crushed for a two-run home run in the seventh.

Japan attempted to rally in the eighth, scoring a run before a botched double steal, uncharacteristic both in its use and execution, helped end those hopes.

In the end, Samurai Japan failed to claim a third title.

“As Koji-san said, we came all the way here because of everyone on this team,” Japan catcher Shinnosuke Abe said. “I personally gained great experience.

“As we played, we became a better team. It’s a shame that the battle ended after the team had become so united, but again, it was a great team.”

The 2013 WBC was a struggle for Japan from start to finish, and didn’t exactly begin on a high note when Yu Darvish and the rest of the nation’s cadre of MLB stars declined to participate.

“They don’t have Darvish, (Daisuke) Matsuzaka, or the stars,” Australia manager Jon Deeble had said after losing warmup games against Japan in Osaka Feb 23 and 24. “They’re going to find it tough. It’s very hard to win three in anything. I think they’re behind the eight-ball trying to win three WBCs.”

Deeble, as it turns out, was right.

The Japanese were uninspiring in their warmup games and needed a three-run rally in the eighth inning to avoid being upset by Brazil on the opening night of the WBC. Japan also had trouble putting away an overmatched China team in its second game.

Japan lost to Cuba to end the first round and narrowly avoided falling to Taiwan to begin the second, needing a two-out, game-tying RBI single by Ibata in the ninth and Sho Nakata’s sacrifice fly in the 10th to win. Back-to-back routs of the Netherlands brought reignited dreams of a three-peat, but the mountain was too high for Samurai Japan to scale.

Without its MLB stars, Japan made due with what it had.

Hirokazu Ibata showed the world the type of player he was by finishing 10-for-18 with four RBIs and a host of clutch hits; Kenta Maeda usurped Masahiro Tanaka as the team’s best pitcher; and Yoshio Itoi hit .286 with a home run, seven RBIs and a 1.024 on-base plus slugging percentage.

“It doesn’t matter how individuals did,” Ibata said. “We only wanted to win the championship. So the result is everything.”

Pitching was thought to be Japan’s strength, and for the most part the Japanese delivered. Even in the finale, Maeda and the Japanese relievers kept the team in position to win until the final out.

What caught up with Japan was its shortcomings at the plate and inability to come up with the big hit.

While Japan scored 26 runs and hit eight home runs in two games against the Netherlands, the team managed 18 runs and no homers in its five other contests. Excluding the games against the Dutch, Japan finished the WBC 10-for-49 with runners in scoring position.

“We need to be better in clutch situations,” Ibata said. “You can’t can get consecutive hits very often, so you need to be able to move runners along.”

The Japanese are feeling the sting of disappointment at the WBC for the first time, after a run that saw the nation reaffirm its status by winning the first two WBCs.

“We wanted to go for the three-peat, but came up short,” Ibata said. “Hopefully, I’d like to give it another shot by getting back here.”