That's the spirit. I was a-hopin' you'd say that. Great. Just use this disk here on Vault City's central computer and then git it right back here. We'll use less uranium, the core won't leak so bad, and this Vault City won't have any reason to come exterminate us.
Speak with Festus, he will tell you to optimize the plant and give you the optimization disk. Afterwhich proceed to Vault City, speak with McClure and run the disk on Level 3 Vault Computer. Return to Gecko and use the disk on the computer console in the powerplant to optimize the plant. Alternatively, you could talk McClure into optimizing the disk for you and save yourself the trouble of heading down into the Vault.
Another NPC in Gecko mentions that if the powerplant is optimized, Gecko and Vault City can trade electricity for medical supplies. Nice thought, but Vault City doesn't agree - if the powerplant is optimized, Vault City invades Gecko, takes control of the city and enslaves the ghouls. There is an option to present McClure with a holodisk showing the power the plant could produce if optimized, and the player can have McClure offer to speak to the Vault City council about a trade agreement with Gecko, but this does nothing to change the result, due to a scripting glitch. Once the plant is optimized, Gecko's fate is sealed. Even changing the outcome of Vault City's dealings with NCR does nothing to change Gecko's ending.