At the Shi temple, you also have to direct fuel along a pipeline to the oil tanker. Go to the Emperor computer, and go into the chemistry database. Choose the fuel option, and direct the fuel to the oil tanker. After you've directed the fuel, go to Chinatown, and talk to Dr. Fung. Tell him that you have a friend who needs help with a spleen. Dr. Fung will charge you $1000. Pay him. Leave for the Brotherhood of Steel building, and heal yourself there. After you've healed yourself, go back to the oil tanker, and tell Chip the good news about his spleen. He'll tell you that he'll be back within a day. After Chip leaves, rest for one day to receive your reward. You'll get some experience points and some information about the lost Arroyo villagers. At this point, make sure that you drop your NPC's off in the ship, and also make sure that you are wearing some form of Power Armor. (You can get a suit from the Brotherhood of Steel building or at Lao Chou's store if you still need one; you should be wearing the other Power Armor that you got in Navarro.)
Save the game, and head to the bridge. Access the computer, and tell the ship to "go." You're on your way to the Enclave base, the final area of the game.