The Marabunta have attacked Lucius Fox's home, and Luke Fox with out his Batwing suit, is forced to attempt to hold off the terrorists by himself. Though fighting as hard as he can, the Marabunta manage to kidnap Lucius, and despite Luke wanting to go try and rescue his father, Batman instructs him to stay with his family, as that's where he's needed.
A few days earlier, Bruce is in the Congo where he inspects the diamond mind he just purchased after the Marabunta were flushed out. While meeting with a government official, Bruce is interrupted by a man named Atticus Fontaine, who represents the parent company of the original owners of the mine, Selcorum, who is so big, and because of the times, couldn't keep track of what illegal activities their employees were committing in the mind. Yeah, okay, seems legit. Fontaine tries to buy back the mine, but Bruce doesn't budge, so Fontaine leaves his card and a vague business threat with Bruce.
Back in the present, Luke is still frustrated that he can't join Batman on the search for his father, so he starts to do some digging as to why the Marabunta would target his father. Luke digs into his father's computer and figures out (while finding out) that it's all about Lucius' connection to Batman's R&D, Wayne Enterprises, and Batman Inc, etc. etc. With the personal matters getting mixed with his "business" end of things, Luke says screw it, and suits up anyways.
Luke convinces Batman to let him in on whatever info he has on his father's location, and the two meet up on a shipping freighter, where the Marabunta have hidden themselves. Somewhere inside the boat, a Marabunta scientist has some contraption on Lucius' head, that's meant to extract his secrets for Batman's tech, so the Marabunta can use it against Batman himself. Well, it's Luke and Bruce's job to stop that, and all goes well until while fighting their way through the ship, they come across the Marabunta's new toy, a giant mecha-ant!