Question: The Lima produces surges that disrupt electronics. Why isn't the Lima affected?
Question: How did the monkeys get onto the space ship and why were they so aggressive?
Question: Tommy Lee Jones killed his crew 16 years ago, but the corpses are still inside the ship, some of them without signs of decomposition! Is not it stinky living with rotten bodies? Why are they still on board?
Answer: He killed the crew by shutting down the life support. The vacuum would prevent them from decomposing. Since he was now a single person, he would not need to regain access to the entire ship.
But one corpse's head was deformed, presumably rotten, while the others were intact. Why is there a difference?
Answer: He also mentions that his last few loyal crew members recently attempted to return home. This is what damaged the reactor and caused the surges. It is likely that these are the crew Brad Pitt encounters.
Question: What was Roy's father doing for so many years? What did he plan to do next? Where did he get all the supplies of air, food, water, etc. to live in the space ship for so many years?
Answer: Clifford was continuing to gather data for the Lima project. He was convinced the project could succeed and that there was extraterrestrial life somewhere in the stars. He was apparently planning on gathering data for the rest of his life. Clifford would have plenty of supplies to last more than a lifetime, considering he murdered everyone else on the team.
Answer: On the way from the Moon to Mars, the Cepheus interplanetary vessel receives an automated distress signal from a Norwegian bio-medical space station (that studies and conducts experiments on Earth animals in the deep-space environment). Apparently, a couple of very powerful and temperamental adult baboons escaped from their cages and killed everyone aboard the space station, feeding on their bodies. When the Cepheus answers the distress signal and arrives at the space station, the baboons attack and try to eat Captain Tanner and Roy McBride, also.
Charles Austin Miller