The Sun says the ex-Blues boss had a clause in his deal which said he had to pay the club £2.5million if he quit.
And members of the board believe that Mourinho feared he would lose against Manchester United and at Valencia in the Champions League without Didier Drogba and Frank Lampard.
A boardroom source said: "Jose met with Roman Abramovich and Peter Kenyon. Roman expressed concerns about the display against Rosenborg. He was not impressed by the way the team was playing.
"There was no indication things had come to an end but later Jose went to see Peter to say he would not be coming to work the next day.
"Peter asked him what he meant and he said 'I'm just not coming in'.
"Peter thought about it for a while then asked Jose if he meant not coming in for one day or forever and said 'Do you mean you want to leave?'
"Jose suggested he would go and Chelsea then told him they would pay him off."