Alexis had yet to learn all the sets of commands that SAM had transferred to her. She was busy with everything else and did not get the chance to do the most important thing that would help them in the current situation - use her super memory to access something that was already in her long term memory.
Alexis tried to access the data but because there was just too much information in her brain, she could not easily locate the list of commands. And in horror, Alexis shouted at the top of her lungs, "SAM, Stop! Stop the engine!"
But nothing seemed to stop. The mechanical whirling sound was still heard and the lights were being lit up in several places that they did not even imagine had lights. And after the start-up sequence was completed, the control panel was now active, and so was the radar system.