This has probably been discussed in some similarity....
When Widmore says everything will cease to be he could be describing what would happen if the two universes collide. Our universe is filled with protons, positively charged atomic particles and electrons, negatively charged particles. The opposite could be true of the flash sideways. When Desmond turned the fail-safe key he was completely exposed to the electromagnetic energy for a moment which caused his atomic particles to reverse polarity. When this happened it pushed him into the FS universe causing alternate conscious to switch and “Flash” back and forth between the universes. At the time both universes were running parallel, all things happening the same. Then along comes Faraday with his Jughead idea. He figures with enough force he can create the Schrödinger's cat situation in which the time lines diverge in each universe. One universe the bomb goes off, the other it doesn't. In the both the FS and current universe Desmond is the potential observer so t! he rules do not apply to him. So far Desmond has indirectly observed the FS, but Widmore WANTS him to directly observe it. He knows that if Desmond directly observes the FS the current universe (positive) universe resets itself to match the FS (negative) universe. Widmore believes that if the MIB goes free, he and the electromagnetic energy on the island will cause the two universes to cancel each other out and everyone will cease to be. The flaw in Widmore's plan is the love Desmond has for Penny. My guess is that he will probably find out in the FS that Penny is either dead or they never met so he will choose the current timeline thereby setting up the final confrontation with the MIB.