The Cortex Prime had malfunctioned. It issued an order prohibiting everyone from investigating the alien spaceship. But the Cortex Prime did not mention that the totaled alien spaceship was flying again. It did not even give instructions on the proper response one should adopt when the alien spacecraft came face to face with the Zenith.
As there was a lack of instructions, the Zenith's autonomous system responded as it should have. When Nolan accelerated towards the space station, a large number of auxiliary devices that looked like antennas on the surface of the Zenith reacted. They spun and aimed at the uninvited guest as sirens blared throughout the space station. A launchpad opened, and a large number of dual-fuselage spacecraft rushed out from the silvery-white Zenith. They fired up their plasma engines and charged at the enemy.