He left Creighton later that year to become special assistant to then Florida Marlins GM Dave Dombrowski, and also coached minor league teams in 1993 and 1994.

One of his first moves provided fodder for critics and boosters alike: late in spring training 2002, he dealt Julián Tavárez and Dontrelle Willis to the Florida Marlins for pitchers Matt Clement and Antonio Alfonseca.

On the downside, Alfonseca struggled while a Cub, and the minor league pitcher traded to the Marlins was Dontrelle Willis, the 2003 Rookie of the Year.

A little more than two weeks after his injury, Hendry sent prospect Bobby Hill and veteran José Hernández to the Pittsburgh Pirates for a center fielder who could replace Patterson for the remainder of the season, Kenny Lofton.

After failing to close out the 2003 NLCS against the Florida Marlins, Hendry made several acquisitions, picking up first baseman Derrek Lee for Hee-seop Choi in a trade with the Marlins, acquiring catcher Michael Barrett in a three-way trade with the Oakland Athletics, giving up Damian Miller in the process and Montreal Expos, signing free agents LaTroy Hawkins, Todd Walker and Greg Maddux.

Injuries to key players like Mark Prior, Sammy Sosa, Kerry Wood, Joe Borowski, and Alex Gonzalez hindered the Cubs during the early part of the season.

Garciaparra missed several games down the stretch because of an injury to his groin, forcing Hendry to sign Neifi Pérez off of waivers.

After in-depth talks with the New York Mets and Washington Nationals, the Cubs sent Sosa to the Baltimore Orioles, getting utility player Jerry Hairston Jr., second baseman Mike Fontenot and pitcher David Crouthers.

He signed middle reliever Chad Fox and traded Kyle Farnsworth to the Detroit Tigers for Roberto Novoa and minor-leaguers Scott Moore and Bo Flowers.

The biggest move was trading three young pitchers, Ricky Nolasco, Sergio Mitre, and Renyel Pinto to the Marlins for center fielder Juan Pierre.

[2] On November 19, Hendry signed[3] former Washington Nationals superstar Alfonso Soriano to an 8-year, $136 million contract to play outfield for the Cubs.

In other moves, Hendry inked Wade Miller to an incentive-laden, one-year $1.5 million extension to stay with the Cubs.

[4] He also signed free agent second baseman and utility player Mark DeRosa (previously of the Texas Rangers) to a three-year, $13 million deal on November 14, 2006.

He completed a trade sending relievers David Aardsma and prospect Carlos Vásquez to the cross-town rival Chicago White Sox for left-handed setup man Neal Cotts.

[6] On December 6, 2006, the Cubs agreed to a four-year, $40 million deal with free agent pitcher Ted Lilly, who played the previous season for the Toronto Blue Jays, beating out the New York Yankees,[7] while Hendry was being hospitalized for chest pains.

On December 9, it was reported that Hendry signed free agent Jason Marquis to a three-year, $20 million contract.

[9] Hendry also signed outfielder/1B veteran Cliff Floyd, a Chicago native, to a one-year, $3 million deal on January 24, 2007.

The Cubs sent utility outfielder prospect Freddie Bynum to the Baltimore Orioles for a player to be named later[11] (right-handed pitcher Kevin Hart).

They selected former number-one Rule 5 draft pick Josh Hamilton from the Tampa Bay Devil Rays and immediately traded him to the Cincinnati Reds for cash considerations.

With new ownership coming at the end of the 2007 season and with the Cubs falling in the standings in May and June, Hendry's chances of staying as the general manager remained an open question at midseason.

Help arrived when Jim Hendry made it clear that the team was a buyer and not a seller with the acquisitions of Jason Kendall, Craig Monroe, and Steve Trachsel.

[13] Japanese superstar Kosuke Fukudome made his arrival to the U.S. and was signed by Hendry to a 4-year $48 Million contract to play right field.

Despite consistently having a team with one of the highest payrolls in baseball, the Cubs struggled in Hendry's final seasons with the club.

Cubs chairman Tom Ricketts notified Hendry on July 22, 2011, that he wouldn't be retained as general manager.