And no one was more shocked than Cruise himself.
"She was talking to Tom on the phone up until last week saying, 'I love you,' " a source tells PEOPLE of the actress.
"Her inner circle has been planning this and switching out cell phones since she was in China [in mid-June]," adds the source.
"When new cell phones arrived, then nobody could reach her. Her old best friends from last week don't have her new number, no email. She's unreachable."
Holmes, 33, also rented her new apartment in New York City in early June. "[Tom] knew that she moved there, but [he thought it was] for different reasons," says the source.
"She said she moved there to drive into the underground garage. There are fewer paparazzi and it's less intrusive for her," says the source. "It was the first phase of getting everything out of the house, and that's why she was able to say she's moving without giving an indication that she was going to divorce him."
Then, last week, her father, Martin Holmes, arrived in New York and helped his daughter clean house, firing many of the people around her shortly before Holmes filed for divorce anonymously in New York City.
Cruise, then filming in Iceland, "had no idea this was coming," a source tells PEOPLE in the magazine's new cover story, on newsstands now.