The episode's cold opening sees Tony and Ziva walking between shipping containers on the docks. Up ahead they see one open: they realize that containers are not unloaded at the dock and pull out their guns and run to inspect the container. Finding nothing inside, they put away their guns. All of a sudden, a firefight breaks out so Tony and Ziva take cover inside the container where they get locked in. The episode becomes the story of Tony and Ziva trying to escape from the container, which is eventually freighted on a truck with them stuck inside. Meanwhile, the rest of the team get worried and have to try to find them. While Tony and Ziva are stuck inside the container, there is a lot of humorous dialogue and banter between them.
Ziva and Tony cannot get a mobile signal from inside the metal walls container, nor therefore can Abby track that signal with a GPS-type reference. First of all they build themselves a defensive barrier with the crates inside the container, with the proviso it won't hold for long if they are attacked with automatic fire. While moving boxes around,they discover what are labelled as explosives, but on investigating, it turns out to be millions in counterfeit money.When Ziva and Tony discover this counterfeit money, hidden in a false wall of the container, they first try burning some in the hope that the smoke (leaving by the ventilation holes) will attract attention. I doesn't, but instead the container is loaded on a truck andthey start dropping the money from the container, leaving a Hansel-and-Gretel trail of money for someone to find and follow them and which is picked up by a drunk.
Meanwhile Gibbs and the team have recruited the aid of the Port Authority security and its chief, to track down the container, little knowing that (this is not revealed till the end) the security chief is in on the corruption himself. First of all, they study the CCTV footage, and manage to work out where Ziva and Tony were before disappearing. They go there and find a body, a bad guy killed in the firefight. They now work out that at some stage, Ziva and Tony must have gone inside a container. But so far there are hundreds of containers with the same company mark. It's gonna take ages to search them all.
Then they realise one of the containers is missing from the real-time photos, so it's been moved, and the security chief tells them that only a few top-loader fork-lift trucks can possibly have moved it (there are no cranes in the vicinity). So the general area of the docks where the container is, is now known.
Inside the container, Tony is trying, with the help some DVD cases in the cargo, Ziva's jewellery and hairpins, to make an antenna for the mobile that will stick out of the ventilation holes.But by now the bad guys have opened up the container; they know Ziva and Tony are inside. When challenged, Ziva manages to shoot the leader (we later learn he's called Wilson) in the foot.They push the antenna out and get a call out very briefly to Gibbs, just enough to tell him the clue of the money, not long enough for their location to be pinpointed, but enough to allow Abby to narrow it down to a 500sq m area.
So Gibbs and McGee are driving to the scene, Ziva and Tony are trying to defend themselves in the container and also buy time by threatening to burn the money. It's just a delaying tactic, the bad guys know they don't have time to burn very much of it. On their way, Gibbs and McGee pass the drunk man picking the money up, and realise they can be directed more exactly by the trail of money than by the GPS fix off the mobile.
Now the twist. Ziva and Tony run out of ammo, but just in the nick of time the dock controller arrives and tells the bad guys to put their hands up. He asks Ziva and Tony to cover the bad guys, but they tell him they're out of ammo. At this point he turns his gun on them and reveals that he is in cahoots with the bad guys, telling Wilson to get the money unloaded. But before he can shoot Ziva and Tony, Gibbs appears behind him and rescues them, and there is a happy ending.
The immediate next bit of the ending is a humorous dig at Ziva, who walks with her legs firmly wedged together, looking for a loo after 12 hours stuck in the container with no bathroom facilities. Finally Ziva asks Tony to dinner, and at this point he realises he was the only one not invited to her dinner party the previous night