You don't need to destroy the gunships, just shoot the balls inside the the portal, then these walls will pop-up, shoot them as well and then enjoy the end game sequence.
At first, at Dark Energy I destroyed the gunships and I was like: "Oh God, what will I do now? If I act too late, the world may end! I cant let that happen! I'm gonna shoot those damn balls at the portal all day!" And I did . When I noticed the shields begun to fall, I destroyed those. Then still nothing else...Then, I noticed that the glowing thing is actually a portal . Then came the "Happy Ending"