Question: What did VOX mean when he said that to find the Morlocks' lair, that Alexander would have to follow the breathing?
Question: What happened to Alex's journals and equations when he left on his trip?
Answer: When Alexander is travelling through time, he sees everything in his lab being removed very quickly, so the equations on his board were most likely erased and his journals were probably thrown away.
Question: When Alex went back in time why didn't we see his machine when 1899 Alex and Philby were talking in the lab?
Answer: He was only focused on saving his fiancée, he didn't think of anything else. If he did he would have thought about it.
Question: What did the Über-Morlock mean when he said to Alexander that the Morlocks would not exist without those like Alexander in their quest for science and technology?
Chosen answer: It was a metaphor for their life. He meant had it not been for the destruction of the planet due to scientists (their creations of bombs, germ warfare, etc), the Morlocks could not have existed because they were a result of the same scientists. Had the scientists attempted to do good for mankind, the world would not have turned out like it did when Alexander visited it.
Question: How is the hologram artificial intelligence system still operational and has power after 800,000 years?
Answer: We don't know what kind of power supply the AI system is running upon, but it's possible it's a system that works on some unlimited energy source that doesn't need fuel or uses very little energy.
Answer: It's a plot hole. Just as, in the original 1960 George Pal movie, the Eloi are still human and speaking 20th Century English. After 802,000 years, all artifacts and traces of our modern civilization will be long, long, long vanished (excepted perhaps for a handful of fossilized bones). Additionally, after such a long time, the human species will probably be long extinct.
Question: When Alex met the Uber Morlock in his sanctuary and saw the time machine running... why was it running? Did Uber use it to go back or forth in time... if so... why and what were its effects? Alex went forward after the fight with Uber and saw the devastation that Uber had warned him about if he were not present to stop the Morlocks by controlling their urges. Then, Alex went back in time, save the girl... then used the machine as a time-bomb and destroyed the Morlocks thereby changing the future.
Answer: The Uber Morlock told Alex to use his machine and go back to where he came from. The morlocks were rulers of the world, they felt Alex was a nuisance. A man who doesn't belong is upsetting the status quo.
Answer: He's referring to the sound that the Morlocks' machinery makes from underground.
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