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NEW YORK -- Jason Bay and the New York Mets missed several opportunities to provide a special ending to a moving night.

It was hard to complain about the outcome, though.

Carlos Pena hit a go-ahead single in Chicago's six-run 11th inning, and the Cubs beat New York 10-6 on Sunday night in a game that ended nearly five hours after the Mets held a touching ceremony to mark the 10th anniversary of the terrorist attacks of Sept. 11.

"It was a little bit different today. Obviously, you could tell the atmosphere was a little bit different. But I think most of us have played in emotional games or seesaw games before," Bay said. "It was actually fun because it was different. Obviously, not fun losing. We had chances but it was pretty special to be a part of."

The Mets' disappointing finish came with nearly all of the 33,502 fans -- several thousand first responders and their families receiving free tickets -- long gone from a game that started at 8:20 p.m. There was a 24-minute pregame tribute to victims of the attacks, their families and many of the first responders that worked tirelessly at the World Trade Center site in 2001.

Making just his sixth big league appearance, Josh Stinson (0-1), the Mets' seventh of nine pitchers, walked Marlon Byrd to start the 11th and gave up a single to Bryan LaHair. Pena singled for the lead.

Pinch-hitter Alfonso Soriano and Darwin Barney each hit two-run doubles off Ryota Igarashi before the first out, and Geovany Soto added a sacrifice fly.

"You keep grinding and grinding," Pena said. "It's not easy."

New York trailed 4-1 after five innings but scored twice in the sixth off Matt Garza. The Mets tied it with an unearned run when reliever Jeff Samardzija made a bad throw on Justin Turner's infield single.

The Mets loaded the bases in the first, ninth and 10th innings but came up empty each time. Ramon Ortiz (1-2) got David Wright to pop out to end the 10th before the Cubs went ahead in the 11th, eliciting mocking calls from the few remaining to bring in an experienced pitcher when Stinson gave up the go-ahead hit to Pena.

"As we went through the ballgame, we had the guys at home plate we wanted to have at home plate several times," Mets manager Terry Collins said. "But we didn't get it done."

The mood was much different before the game. With the stadium lights dimmed and fans holding electronic candles in one hand and many using the other to take photos with their phones, the Mets held a dignified ceremony that included members of the 2001 team that played in the first professional sporting event in New York, 10 days after the World Trade center collapsed.

Players from the Cubs and Mets escorted members of "Tuesday's Children," a charity for families affected by the attacks, onto the field, where they lined up among the uniformed emergency-service workers on the first- and third-base lines. A 100-by-300 foot flag was held by 225 first responders and victims' family members from "Tuesday's Children."

"It was really, really well done," Collins said. "Even Mike Piazza, standing next to me, said, 'Boy, isn't this beautiful out here. What a nice tribute.' I think he's absolutely right."

Marc Anthony sang the national anthem, as he did on Sept. 21, 2001. Piazza, who hit a rousing two-run homer in the eighth inning to help the Mets beat the Atlanta Braves that night, caught a ceremonial first pitch from John Franco, a teammate on the 2001 squad.

There was no uplifting ending this time for New York.

The Cubs scored late in each of the three games, losing the opener Friday, but winning the last two to take their first series in New York since 2006.

"We don't do things the easy way, that's for sure," Cubs manager Mike Quade said. "They kept playing, they kept battling."

Mets players briefly considered defying Major League Baseball's policy by wearing the caps they wore pregame honoring New York City's emergency-service units during the game.

"What are they going to do, fine us?" catcher Josh Thole said before deciding against it.

Joe Torre, MLB's executive vice president for baseball operations, told The Associated Press the decision was made to keep policy consistent throughout baseball and that "certainly, it's not a lack of respect."

Between innings, the Mets played videos on the main scoreboard that paid tribute to the recovery efforts. They also thanked the 2001 squad's manager Bobby Valentine, who was not able to participate in the pregame ceremony because he was part of the ESPN broadcast team for the game.

American Idol contestant Pia Toscano sang "God Bless America" during the seventh-inning stretch, standing with several uniformed first responders around Major League Baseball's red, white and blue logo that was painted on the grass in front of the Mets dugout.

Mets starter Miguel Batista was with the World Series champion Arizona Diamondbacks in 2001, and made two appearances in the stirring series against the New York Yankees that inspired the city. He threw 7 2/3 shutout innings in Game 5, won by New York in the 12th inning. He also got one out in Game 7.

On Sunday, though, the 40-year-old journeyman, making his third start for the Mets, struggled with his command. He walked three in five innings, hit two batters in the third and gave up four runs and five hits.

Garza gave up three runs in seven runs, walking three and striking out four.

Jason Pridie hit a two-run shot in the 11th.

Game notes

Mets reliever Bobby Parnell said his dad, a fire chief in Salsbury, N.C., recently received a piece of steel from the World Trade Center site that will be used in a memorial. ... Quade, who was a coach with the Oakland Athletics when they played the Yankees in the 2001 playoffs, deliberately didn't visit the site on this trip. "I did not want to get angry again," he said. ... Mets LHP Johan Santana will make his third rehab start this week for Class-A Savannah in the South Atlantic League's championship series. He threw three innings in his previous start for Savannah. Collins said he should pitch four innings this time.