You can't do this with a segue. Segues can only be made between controllers in the same storyboard. The only way to do this, is in code by instantiating that first controller, and setting it as the window's root view controller.
UIStoryboard *sb = [UIStoryboard storyboardWithName:@"SomeOtherStoryboard" bundle:nil];
NewController *new = [sb instantiateInitialViewController];
self.view.window.rootViewController = new;