That offseason, the Cubs spent $300 million on free agents, and in 2007, it paid off as they won the National League Central. It was the second of three division titles for the Cubs under Hendry, but it wasn't enough.
On Friday, Hendry was dismissed as the Cubs' GM, a job he had held since July 2002.
"At the end of the day, I'm not going to leave with any problems," Hendry said. "We just didn't win enough ballgames, that's the bottom line. It's professional baseball. You don't win enough games over a couple years, you can't fight change."
Cubs chairman Tom Ricketts actually told Hendry that he was going to make a change on July 22 before the team played the Astros at Wrigley Field. Hendry had the choice of leaving then.
"At that time, we decided it was best for me to stay on," Hendry said. "We had [the Trade Deadline] coming up, we had a lot of Draft choices that needed to be signed. We both felt that possibly me staying through that gave us the best chance to sign the players."
As for the Trade Deadline, Hendry said he considered some moves but wanted to let the next GM make the decisions.
"It would have been easy to trade a few guys to look like we were clearing the deck, or 'Jim's cleaning house,'" Hendry said. "A few guys may want to be here, and the next general manager and Tom may want them to be here. It's a real important winter, and moving forward, the next person ought to be making those decisions on some of these guys and that's why I didn't trade them."
Even though he knew it would be awkward, Hendry remained loyal to the Cubs in his final weeks on the job.
"I care too much for the people who work under me," he said. "It would've been shameful if [my leaving] got to be an issue or that got to be a big story."
In an emotional news conference, Hendry credited Andy MacPhail for giving him the GM job with the Cubs and cited several others who have helped him, including longtime super scout Gary Hughes, currently a special assistant. Hendry had gone from baseball coach at Columbus High School in Miami to the head coaching job at Creighton University when Hughes and the Marlins hired him for their scouting department.
Hendry likes to tell a story from a Marlins Draft, when Hughes called him into the war room in the middle of the 11th round. Instead of asking Hendry for advice on the next pick, he was needed to go fetch some fat-free fig newtons.
"I was 'Joe hot-shot college coach,' and four years later, I ended up here, running the Minor Leagues for the Cubs," Hendry said. "I was a very fortunate guy."
Now, he's looking for work for the first time in his life.
"There are a lot of huge decisions that have to be made this offseason," Hendry said of the Cubs. "If I was the one making them and they all didn't work out, then the person after me would have to wear some of those.
"In his heart, [Ricketts] wanted it go to better," Hendry said. "He didn't take over this franchise looking to think [I] would be a short-termer. It's big business. We're here to win games, and the last couple years, we didn't win enough of them."
Now, he will be able to devote more time to his children, Lauren and John, who got the news Thursday night.
"I'll hopefully be a better dad -- I've got two great kids and I need to spend more time with them," he said.
Hendry expected to take some time off and added he's not ready to retire.
"I will leave here with nothing but gratefulness to have been to be part of an organization for 17 years," he said. "Not many get to do that. Not many get to be the GM for nine [years] without a World Championship. I got more than my fair chance to do that. I'm disappointed in myself that we didn't do it in the first five to seven years when I thought we could."
There were mistakes. The Cubs struggled to find the right pieces and some definitely didn't work -- remember Milton Bradley?
"I tried to, on a daily basis, do what I thought was best for the Cubs and I did try to make decisions based on what was good for the organization," Hendry said. "You always look back on your mistakes and want mulligans, and just like most things in life, you don't get them."
Even though he knew that he wouldn't be retained, Hendry did not lose his passion for the Cubs.
"I tried to focus on what was at hand," he said. "It was good for me -- I was still throwing stuff in the [suite] when we were losing games and pacing around watching [Carlos] Marmol in the ninth a couple times. I didn't really change much, which was good."
It was difficult to address the team on Friday, and Hendry admitted to not looking some of the players directly in the eye.
"I had my moments by myself," he said. "I felt like I couldn't have a crack in the armor in the clubhouse to Mike [Quade] and his staff, to players before the Deadline. I had the same conversations I always did.
"I don't think [Ricketts] ever set out wanting to do this," Hendry said. "We just didn't win enough games."
Carrie Muskat is a reporter for MLB.com. She writes a blog, Muskat Ramblings, and you can follow her on Twitter@CarrieMuskat. This story was not subject to the approval of Major League Baseball or its clubs.