This mission is within level 4-4. You must speak to Miss Ion and she will give you 3 numbers. You must then find the missile room and press Use against each number in the order she gave you. Then go back to her and get 3 more numbers. Repeat the input process and return to her for the final 3 numbers. Once you input the final number, walk up to the missile and press use on it to deactivate. You can then return to Miss Ion to complete the mission.
Note she will only tell you the numbers once. So do not talk to her whilst putting out fires. If you miss the numbers then you will not be able to do this as putting in the wrong number will void the mission and it is highly unlikely that you will guess the 3 numbers in order out of 9 possible.