filling in for Crisp and J. D. Drew in center and right field. Peña hit a grand slam off closer Chris Ray of the Baltimore Orioles to help the Red Sox to a 5–2 victory on April 26. Throughout the season, Peña was rumored to be on the trading block, including a deal at the trade deadline that failed to go through. Washington Nationals On August 17, Peña was traded to the Washington Nationals, with the Red Sox receiving 25-year-old first baseman Chris Carter and the Arizona Diamondbacks receiving Emiliano Fruto and cash considerations from Washington. Peña hit well for the Nationals, and finished 2007 with a cumulative 289 at-bats, 13 home runs and he batted .259 with a .319 on-base percentage and a .439 slugging percentage. His $2.3 million signing bonus is now the third largest ever for an amateur free agent. In December 2007, he signed a one-year contract with the Nationals for $2 million with a mutual option for 2009 of $2 million. On March 28, , Peña was designated for assignment by the Nationals and placed on waivers. Peña went unclaimed and declined an assignment to the minor leagues so he was unconditionally released. New York Mets On April 20, , Peña signed a minor league deal with the New York Mets and was assigned to Triple-A Buffalo. He was released on June 22, 2009. Bridgeport Bluefish On May 30, 2010, Pena began playing for the Bridgeport Bluefish, an independent team in the Atlantic League. In 38 games for Bridgeport, Peña hit .310 with 8 home runs and 38 runs batted in. During the offseason Wily played for the Tigres del Licey of the Dominican Winter League. San Diego Padres On July 19, 2010, Peña was signed to a minor league deal by the Padres and assigned to Triple-A Portland. Arizona Diamondbacks Peña signed a minor league contract with an invitation to spring training with the Arizona Diamondbacks prior to the 2011 season. As of mid-June, he was hitting .356 with 21 homers and 62 RBIs for the team's Triple-A affiliate in Reno. He was called up on June 21 and hit a home run that night in his first major league game in 3 years. In a game against the Detroit Tigers on June 24, Pena launched a go-ahead homer an estimated 454 feet deep into the left-field seats at Comerica Park to give the