User blog comment:JakePT/Lair of the Shadow Broker is INCREDIBLE/@comment-1900300-20100909121742/@comment-217683-20100909192321

The Cerberus operatives are ultimately loyal to Shepard because Shepard is the only reason they're alive, eh? If that's how it works, then Shepard is ultimately loyal to Cerberus, as Commander Shepard is only alive because of Cerberus.

I agree that some of the crew were won over and would side with Shepard over Cerberus, but you simply can't say that the entire crew "owe the Commander everything and are ultimately loyal to Shepard" with no evidence to back that up. The Illusive Man isn't an idiot. He likely made sure that at least some of the Normandy's crew were die-hard loyalists of the type described in Retribution.