First go to the planet Mylon and then get out your flux rifle. Then go to the very end of the platform at the very beginning of the level. Next shot both of the robonoid commender's. It will take some time to beat them but each shot upgrades your rifle to the v3. Then it takes 2 shots. If they both die (they will)just jump off and start over. Just keep doing this till it is upgraded all the way.