Before you start this mission, make sure you have the Beam Cannon equipped. On level 3, quickly defeat the green Zakus and leave the red one alone for the moment. Make sure you get them all before continuing. After you defeat all the green Zakus, jump on one of the tallest buildings you can find that is fairly close to the white base. Two bombers will approach very close to the buildings -- close enough so that you can jump from the building to the bomber. After jumping on the bomber, switch to your Beam Cannon and aim at the back stabilizer (the large fin on the back of the bomber) and hold Square for about two seconds. This will release a more powerful blast from the weapon.
Firing this blast two times at the back fin will destroy the plane and it will start to fall. Repeat this for the second bomber. Note: This requires practice.