If you search for fares on Expedia.com right now, you’ll probably see fares from all the big carriers like United, US Air, Continental, Delta. But you’ll really have to dig to find fares from American Airlines. They’re way at the bottom and visible only if you click on a link. Expedia is punishing American. But what’s odd is that they’re punishing them for what American did to… Orbitz. Expedia’s competitor! American recently pulled out of Orbitz and Expedia is aligning itself with its rival as part of a struggle to not let airlines have any more control over how people book tickets.

Airlines make payments to intermediary companies to bring their fares and flight information to the travel websites. But that gets expensive and lately American has wanted to skip the middleman and make sites like Expedia more of a gateway to AA.com where they can sell customers not just the fare but baggage fees, seat upgrades, flight insurance, car rentals, hotels, all sorts of add-ons. The websites meanwhile want to be in charge of who’s selling what and make their own commission on those sales.

We talk to Ben Mutzabaugh who covers the travel industry for USA Today. He details the showdown going on right now.

We’re also joined by Douglas Quinby of the travel research company PhoCusWright. He sees the war eventually dying down as both airlines and travel sites realizing they exist symbiotically and that customers will punish them for not sorting it out.

Also in this show, the band Gorillaz releases a new album recorded and mixed entirely through iPad apps.