At first, Phelps felt frustrated by his coach's absence.
"I thought if he didn't stick it through, why should I have to show up for practice?" he says. "But I think we both used that time to learn a lot about ourselves and to change the way we related. It was painful but worth it in the end."
Looking back, Bowman says, he would have handled the entire period differently, pushing Phelps more judiciously. "I kept telling him, 'You're never going to get there. You'll never be in shape. You're so lazy,'" he recalls, pounding his fist into his palm for emphasis. "And surprise, he didn't want to come to practice."
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When Bowman backed off, Phelps picked up his work.
In some sense, he was right to be concerned, though. Phelps could not smash the competition at the Olympic Trials and bounce back a month later to do the same in London. He was not as fit as he had been for Beijing.
But he still had as good a meet as anyone, still won his last individual race and last relay. Bowman's face brightens at the memories of their final days as teacher and pupil. "The way it ended up was great," he says.
Urbanchek, who first met Phelps and Bowman when they arrived together to train with the national team before the 2000 Olympics, reveled in those final days watching what he believes was greatness bred from chemistry that couldn't have been replicated.
"You hear people say anybody could have coached Michael Phelps," he says. "That's [not so]. I'm the first person to say that I feel I know how to coach champions, but only Bob could have done what Bob did with Michael."
"There's zero chance anyone else could have taken me where Bob did," he says. "Zero. I've thought about it so many times. I've thought about so many other coaches. Bob just knew me the best, had me figured out. I owe him so much."
Post-Michael life is easier in many ways. Bowman used to begin every meet by plotting with organizers how Phelps could enter and exit without being mobbed. He had to have someone watch Phelps' water bottles so no one would steal them.
Now, he can just show up and coach.
He's different with his swimmers, too, less of a blunt hammer.
"I hear he's smiling and laughing on the deck," Urbanchek says. "That's not the Bob I know."
That guy was right for some competitors, including the young Phelps, who would take on any demand, no matter how arduous.
But in dealing with post-Beijing Phelps, Bowman had to expand his kit of coaching tools. He shares an anecdote from a recent training session in California to illustrate his maturation.
One of his swimmers, Annie Zhu, had just completed her endurance laps, and Bowman pointed her to another lane for further work. She shook her head and said, "I'd really rather not."
The younger Bowman might have tossed Zhu on the next flight home, her ears ringing from a scathing lecture about lack of commitment. "I would've used a nuclear bomb to kill an ant," he says.
The current Bowman? He shrugged it off and told her to get her tail in the pool, which she did.