A missed check-in with ATC could have been the first clue that something was wrong. I don't know the time intervals they use. A lightning strike may have caused the airplane to lose it's radio initially, and then things got worse. The PIC (pilot-in-command) can deviate from the flight plan if needed - such as to avoid weather. Depending on where they are or what the immediate problem is, ATC permission may not be needed, or the PIC may have had to deviate after losing the ability to communicate with ATC. The South Atlantic is still a pretty desolate area.
The media reports are all pretty poor. Even the experienced pilots on the avsig forum are scratching their heads.