Getting back to my point. Let's start by examining the way team communications should work. The team starts out in constant communication with the ship, which is the kind of protocol I would demand if I was monitoring the team from the safety of the ship. Everyone online all the time. Any loss of communication and I'd yank that team out. No questions asked. You stay in communication or you don't get to come on a mission years out into space again. Ever.
That's the very way that the expedition team started out as they explored the underground and unknown complex, and then...they split up. It was suddenly Shaggy and Scooby on their own.
What captain, team leader or just plain everyday person worth their salt splits up on a planet containing only 17 crew members facing the unknown?
That's because it was an ad hoc team with what seems to be little to no pre-planning, hell most of the team didn't even know each other prior to waking up from hyper-sleep. Then once on LV-223 it seemed to me that Halloway was just so damned eager to get going that he didn't bother with any sort of meeting to go over protocols, just grab you stuff and go. Add to that there was no clear chain of command either; Janek was in charge of the Prometheus but his authority didn't seem to go far outside of its hull, Halloway and Shaw were in charge of the expedition but they didn't choose or assemble their team, that was done for them, then you have Vickers who seemed to be in charge of the whole show or at least had the last word in everything but she was neither an expert on the Prometheus or some sort of experienced survival or expedition leader.
Worse than this, and for reasons never explained, the biologist and the geologist got lost. The place is mapped for them in 3D...and they got lost. They geologist himself mapped the place...and they got lost. They're in uninterrupted communication with the team underground and the ship...and they got lost. The ship was monitoring all of them on camera and radio...and they got lost. They wandered down a few corridors traveling in very set directions...and they got lost. They could have called anyone at anytime and asked for directions...and they got lost. They heard the warning that they had to get back to the ship ahead of the storm...and they got lost. Did they forget how to call the ship (what with only one ship they could call)? Did the ship forget them (because 17 people are too hard to monitor)? Did the team forget them? Doesn't matter. They got lost.
Then, despite the unexplainable reasons for them getting lost, the crew on the ship decided to abandon them. They didn't leave a guy on the bridge to monitor their safety, no matter how tenuous the communication might have been. They simply wished them luck and abandoned them with no more concern than two guys who missed a connecting bus. This plotless decision, which is soundly outside the realm of good judgment, is a turning point for me in the film.
This is probably one of the biggest misunderstandings of the movie next to the confusion of LV-223 for LV-426, the geologist did not personally map the complex himself, he merely sent off the probes that did the mapping. At no point was there any indication that he was able to view the data from the probes from where he was, it appeared that the data was beamed back to the Prometheus and could only be viewed there.
I will grant you that the lack of concern over them being lost did seem odd to me too. Janek's apparent lack of concern had me initially thinking that he was in on the real reason for the mission and was a company man through and through. Obviously he wasn't aware of the true nature of the mission and was definitely was not sort of company lackey which does make it hard to really explain his lack of concern over the two lost boys. Then again, they really weren't his concern in a manner of speaking, after all, the ground mission really wasn't in his purview, they were Shaw & Halloway's people essentially and as a result, their responsibility.
The biologist and geologist were soundly against going anywhere near an unknown life form. They purposely went East to avoid the 'life form' detected to the West. And who wouldn't? Alone on an alien planet in alien ruins surrounded by alien dead ANNNND cut off from the ship both in terms of distance and by communication. I'd go East. Can I see a show of hands of anyone who'd go West without sufficient safeguards while lost underground in the dark and subsisting on canned air?
Then...
...they got caught in the room of oozing pots and the giant head and a freakish, faceless, albino snake slithered right up to them to say 'hello'.
Suddenly, the biologist wanted nothing more than to give a large glistening, slithering, tentacle worm a hug. The hell...? Did his healthy respect for the unknown, and therefore potentially dangerous, go right out the window in a place with no windows? There are insects no larger than a freckle that can pass diseases to you and me on Earth, but this guy reached out to a tentacle in a posturing stance that just screamed dangerous. Had this 'biologist' never seen a cobra, timber snake, rattler, or any other creature I could name demonstrate predatory posturing? Never mind that it had no eyes and nothing that would have communicated 'safe to touch'. Never mind that it came right up to him, which is generally a sign of fearless disdain or hostility in an animal sense. Never mind that he had
NO IDEA WHAT IT WAS! It could have been as harmless as an earthworm, but it was the size of a vacuum hose! How thin was the air in his helmet that he would suddenly switch from his 'East not West' policy? The geologist was stuck in a helmet choked with hash, but the biologist was...what? Bipolar in his respect for the unknown? Selectively careless in the case of alien cave snakes?
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This one I'll grant you without argument, there is no real logical explanation for this one except for convenience of the plot. Of all of the so-called inconsistencies or plot holes in the movie this was the one that I couldn't understand or explain in any logical or meaningful fashion and was a definite WTF moment for me.