I think I got it. Here's the code for anyone who needs some help with this in the future:
boolean run = false; boolean run2 = false; do { System.out.println("Introduction."); System.out.println("Menu 1 ( 1, 2, or 3)"); int menu1 = input.nextInt(); if (menu1 == 1) { do { System.out.println("Menu Level 2, option 1 - Select next level: ( 4, 5, 6 (Go back)"); int menu2 = input.nextInt(); if (menu2 == 4) { System.out.println("Menu 2, option four."); } else if (menu2 == 5) { System.out.println("Menu 2, option 5"); } else if (menu2 == 6) { System.out.println("Breaking out of menu level 2, going back to menu level 1"); break; } } while (!run2); } else if (menu1 == 2) { do { System.out.println("Menu Level 2, option 1 - Select next level: ( 4, 5, 6 (Go back)"); int menu2 = input.nextInt(); if (menu2 == 4) { System.out.println("Menu 2, option four."); } else if (menu2 == 5) { System.out.println("Menu 2, option 5"); } else if (menu2 == 6) { System.out.println("Breaking out of menu level 2, going back to menu level 1"); break; } } while (!run2); } } while (!run); } }