"He asked if he should accept it," Manuel said the other night, explaining that Thome had a lesser offer from the Indians, the team he grew up with as a big leaguer. "I told him to go for it, to think about the security of his family."
Thome took the offer and became the cornerstone of the resurgence of Phillies baseball. He spent three seasons in Philadelphia before being traded to the Chicago White Sox in 2006 to make room for Ryan Howard at first base.
Now, with 604 home runs and at 41 years old, he's back with Manuel, who's his manager with the Phillies for what is undoubtedly his final season. Five years after this, he'll go into the Hall of Fame on the first ballot -- and wearing an Indians cap on his plaque.
Each time I talk with Thome I remember a story his dad, Chuck, told me years ago. As a youngster, Jim was a diehard Chicago Cubs fan, and since he was from Peoria, Ill., Wrigley Field wasn't that far away.
When Jim was 9 or 10, Chuck said he and his son went to a Cubs game early and somehow the young Thome managed to get in the dugout.
"Dave Kingman was his favorite player and Jim wanted to get his autograph," Chuck related. "The sad thing that day was Kingman more or less blew him away. Barry Foote, the catcher, saw what happened and managed to get most of the Cubs to autograph a ball for him.
"From that moment on, Jim promised that if he ever made it to the Major Leagues he'd never turn his back on people seeking his autograph."
And he never has.
Thome, who signed a one-year deal for $1.25 million, is back for a final chance to win a World Series title.
The Phillies and Manuel are hoping he can provide left-handed power off the bench and play first base once or twice a week, especially during the absence of Howard, who's recovering from a ruptured Achilles tendon.
Thome has played fewer than 30 innings on defense since he left the Phillies , but each morning during Spring Training he works hard taking ground balls and has been playing the position in Minor League games.
"The Phillies have set the bar very high," said Thome. "This is as good a place in baseball right now to be in."
A few days ago, the Twins played in Clearwater, Fla., and it was amazing the emotions the Minnesota players showed when they spotted Thome during batting practice.
"He's one of the greatest people I've ever been around, and that says a lot, an awful lot," said Twins skipper Ron Gardenhire, who managed Thome in 2010 and until Aug. 25 of last season, when the slugger was dealt to Cleveland.
Former Twins closer Joe Nathan said "Jim Thome is the world's nicest man. He's one of those guys that the hype is so great before you meet him, then he lives up to the hype -- and more!"
During the reunion with his former teammates, Thome told them, "if it got to January and February and a team hadn't called, I was very content on retiring. I know you can't play forever."
"The key," Thome explained, "is getting my body to react again to playing the field and being out there more than I've been out there [at first base] in the last six or seven years."
Manuel recently recounted the first time he met Thome, who was 19 at the time.
"I look at Jimmy as my son," said the Phillies manager, who became Thome's mentor in the Indians' farm system and later in the Major Leagues with Cleveland. "I keep telling him he's my son. I met him when he was 19. He was kind of shy -- I guess you could call it naïve. He didn't have a lot of confidence then. He's come a long way from his first year."
In 1991, Manuel was Thome's manager at Colorado Springs, and it was that summer Thome was named the American League's top hitting prospect by Baseball America. That was also the summer, with Manuel's coaching and coaxing, that Thome made it to the Major Leagues for the first time. He played in 27 September games and got the first of his 604 home runs. It came against the Yankees' Steve Farr on Oct. 4, a two-run shot in the top of the ninth inning that gave the Indians a 3-2 win.
"I often think back to the years I was with Charlie when he worked with me in the Minors as a hitting coach, and when he was managing the Indians," said Thome. "There were a lot of ups and downs, a lot of grinding it out.
"He's a very good baseball man in all aspects. He can pick out the little things in your swing and work on them with you. He has that special knack."
Manuel said he and Thome often sit in the dugout together, and if the conversation could be taped it would be priceless.
"He'll whisper something to me about a player or the game," said Manuel. "Sometimes it might be an interesting fact about the game, or maybe something humorous. It never gets old."
Thome played in the World Series for Cleveland in 1995 and '97, when the Indians lost to Atlanta and Florida.
Now, he's back with the Phillies and said "everyone knows my dream is to win a World Series, but to be back with the team I left Cleveland for is very special."
Nothing would be more fitting for that dream to come true with Thome and Manuel wearing the same uniform.
Hal Bodley is the senior correspondent for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.