The actress, 33, was increasingly unhappy in her five-year marriage to Tom Cruise as she realized "she no longer had the life she wanted, in terms of her career, her way of life, everything," a source tells PEOPLE in this week's cover story.
So she took action – quickly.
"Once she decided to go, she was done," says the source.
With help from her unflinching attorney father Martin, she orchestrated a secretive exit strategy that included moving into a new downtown Manhattan apartment, switching cell phones and keeping her megastar husband in the dark – until a bombshell phone call in which she broke the news to him.
"She knew she had to have everything locked down before she pulled the trigger," says the source, "because there could be no wiggle room if she didn't want this to turn into a long, drawn-out battle."
The strategy worked, and on July 9 – just 11 days after Holmes revealed her divorce filing – lawyers on both sides announced they had reached a lightning-fast settlement that sources say gives Holmes what she wanted most: primary custody of their 6-year-old daughter Suri.
Cruise, 50, will have generous visitation rights.
The still-stunned actor "was a happy man and thought he had a happy life," says another source. "He keeps asking, 'What's happening?' "
For much more on why the marriage crumbled, the phone call that ended it all and what role Scientology will play in Suri’s life, pick up this week's issue of PEOPLE, on newsstands everywhere Friday