The 50-year-old megastar, who was blindsided when his wife of five years, Katie Holmes, filed for divorce on June 28, "was thinking, 'What did I not see?' " a source who knows the former couple tells PEOPLE in this week's cover story.
Especially tough: His month-long separation from 6-year-old daughter Suri, which finally ended when the pair reunited on July 17 in New York City.
What took so long?
"He's wanted to see her as fast as possible since this started," says a source, who cites Cruise's obligation to his sci-fi thriller Oblivion as the main obstacle. "He couldn't shut down production, cost people their jobs. People count on him."
In agreeing to a divorce settlement in a mere 11 days, "Tom tried his best to do what's right for Suri," according to his longtime friend and lawyer Bert Fields, who says the star is "sad" but not "bitter" about the situation.
Cruise has been leaning on his older children, Connor, 17, and Isabella, 19, his three sisters and his mother – all of whom share his Scientology religion. Several members of his family joined him for support as he filmed his final scenes for Oblivion.
"Tom is not ashamed of his beliefs," says the source, who knows the former couple, "and won’t hide them from his daughter."
For much more on this story, including details on Tom's trusted inner circle, how he’s coping and Holmes's new life, pick up the new issue of PEOPLE, on newsstands Friday