After boarding the mothership after the previous event. You will have to turn off 6 engines. As you turn off 5 a cutscene will be triggered and you and Zola will split up. Go through the portal and then before you board the mechat ship, save and then jump on. Remember, don't choose easy mode and watch the tutorial so you know what you're doing. Shoot the missiles out the sky with the guns (don't overheat them) and them lock on with the missiles to take down Nene. He starts at the front until he takes enough damage then goes to the back and sides until he takes enough damage and then finally he appears in front.
Time in: 12-14 hours approx
Note: Save point just before