Unless you are the second in command, there may well be a boss who feels threatened by your skills and ability...They can and do eliminate employment assets...Not to mention personality conflicts...
In your example, the one who is second in command is better off moving on. If he's good enough to be second in command, he's good enough to work just about anywhere and who would want to work for a company with a CEO who is out to eliminate threats to his own position as opposed to making his company as successful as it can be?