Continuity mistake: When Travolta and Jackman are chased by the vans, there is a shot from Travolta standing in the car with a gun in his hands. A split second later there is a shot from the front, showing them sitting next to each other in the car. There's no way he could have gotten down so fast.
Continuity mistake: When the government agents try to take out John Travolta and Hugh Jackman, all of the SUV's are supposed to be Lincoln Navigators. Travolta destroys the first two. The third SUV turns left around a corner and it's a Ford Expedition, not a Lincoln Navigator. The scene cuts away and when the SUV is closer it's a Lincoln Navigator.
Answer: JT is exactly who he says he is. He leaves a body behind to fool the FBI/CIA into thinking he is dead. Jackman would have believed it too had he not seen him heading down the stairs and the surgically altered corpse. Berry was not hurt, the wire, the DEA story and her getting shot were all parts of a ploy for Jackman to trust and confide in her, making it easier for Travolta to make Jackman do what he wanted. Travolta didn't actually kill any hostages directly himself, (though he did put them in that situation, he is by no means Mr. Innocent) - had the police done what he asked, no one would have been hurt at all. So basically, he IS a good guy, but his methods are somewhat morally lacking.
Grumpy Scot