Again earth is in severe danger and needs to be rescued - so far, so good. Again the rogue scientist is up against the establishment... well you know the rest. All this could make up a good movie, but as all normal, unlikely disasters have already been put on screen, a new event needed to occur... Put short: I would fire the scientific adviser (if there was any at all) - science fiction usually does not need to care much to obey existing science but when a story is being formed around known scientific processes, errors in logic hurt the educated viewers ears and eyes.
Some of the flaws (taken from the German version, maybe some are just translation problems?): No methane has ever burned without oxygen - certainly not in 80 miles altitude with a partial oxygen pressure in the range of that of a normal (not a high) vacuum on earth... No ozone layer ever has saved earth from any coronal mass ejection, nor could it ever do that, nor does it have ANYTHING to do with the effects described in the movie (it "saves" earth from EM UV radiation, nothing else)... No magnetic (->Van Allen) belt is located below the altitude the MAV ever obtained... and so on. The list of obvious factual errors is endless, very disturbing for any sci-fi fan who has an interest in real science, rendering the "PhD" guys in the movie to clowns.