Jack: Tony, it’s Jack.
Tony: Jack, I’ve been monitoring the FBI bandwidth. What the hell’s goin’ on?
Jack: Listen to me, I need your help. Where are you?
Tony: 3rd Street and B.
Jack: OK, listen to me, I need you to meet me at the Port of Alexandria. I need you to bring our weapons and a surveillance package. Get there as soon as possible.
Tony: Jack, wait.
Jack: I can’t. I’ll get back to you as soon as I’m en route.
(Special thanks to AlmeidaIsGod[dot]com for the verbatim transcript).
The red text is key here. Jack tells Tony about the Port of Alexandria, and this immediately makes Tony say "wait." That line always stuck out to me but now it's starting to make sense.
Tony wanted the weapon all along. And it's likely that Tony knew of the bioweapons coming into the Port before Jack even called him. So, what do you think Tony was thinking when he told Jack to wait? Was he going to tell Jack something about those weapons before Jack cut him off? Was Tony initially willing to fill-in Jack on this separate agenda?
Think of it this way- Tony never wanted Starkwood to have the weapon. He went way out of his way to blow up Starkwood's supply (for what we thought were the obvious reasons at the time). So, is Tony working with/for someone else? Why does he want the weapon? These questions will be answered, but until then we cannot assume Tony is evil. He certainly was not in league with Starkwood. There's an unknown player or group involved, I'm betting. Killing Larry Moss is bad (I think he's really dead, but I know a lot of you think he and Tony staged it on the fly). But if Tony is wrapped up in something more dangerous, Moss' death may have been a necessary evil. Let's wait and see.