nice theory

but then do i still wonder why you would make place in a temple for your enemy and what the skaarj by the pool of thunder was doing there anyway, waiting for someone to go for a swim in a pool to attack him? must be a pretty boring job
but on the other side, alot doesnt make sense: why didnt the nali never use the weapons they own?, how do those doors close without having to push them back?, why does the nali on nali castle get killed by a ship? was it really worth the ammo?, what are the skaarj doing in a temple?, why is belt tower in bluff eversmoke placed on such an illogical place?, if the water god can make lightning to crush wooden pillars why doesnt it just use it to attack the skaarj?, why do you get killed when you touch the torches in the secret grave in harobed?, how does the dispersion pistol recharge? what is the point of all those useless stuff when you are escaping with the escape pod?
and i can come up with a whole lot more

ofcourse am i just nit picking for the fun, and am i aware that this is just a sience fiction game and that not everything is supposed to make sense. but that doesnt mean it isnt fun to think about it

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The Skaarj was there for the same reason that Skaarj at the beginning of Chizra was there: exploration. Probably got lost in the old temple.
Nali are a peaceful people, they do not use violence, instead they pray to their gods.
It's a foreign planet. It could be some field that detects lifeforms and some strange energy moves the door/magic. Wouldn't be that strange, Nali can teleport when meditating (although I'm curious if it isn't really teleporting and if they maybe enter their "paradise" and are dead in that manner or if they have some destination on Na Pali they teleport to). Maybe the door works with floor plates which trigger a mechanism but the moving floor plate you step onto is not displayed due to the limitations of the engine. Movers can cause BSP holes in UE1 after all.
It got killed because it escaped its duties and because it was helping a human. You were next to the Nali when it happened after all and the ship most likely saw you two.
Skaarj show no mercy, ammo doesn't matter.
The Skaarj are exploring the temple, collecting information about the Nali and their knowledge of the planet and searching for resources to repair their mothership I guess.
The tower could have been built at the end. There is not much place to build stuff in Bluff Eversmoking. There is just the cliff the cloister was built on and that one island where the tower was built on. Imagine they built the cloister first on that cliff (for aesthetic reasons) and realized they had no room to build the tower there too. Or maybe there was an earthquake which caused a landslide so the room they reserved for the tower was gone so they chose that one little island? Again, many possibilities to interpret this.
The lightning was created by a (Tarydium?) crystal if I recall correctly. Due to its force I assume the Nali are afraid of it or something of that kind and since it's almost like a weapon and as Nali are peaceful and do not use weapons I guess this could be another reason why they do not use it to kill the Skaarj.
Torches with BSP holes. Sounds logical to me.
I guess it drains energy from the environment or something of that kind.
It will make some sense, the lasers and all that stuff was probably some last try to keep you from escaping the mothership/to kill you. Another reason could be a (due to the destroyed core damaged) laser forcefield similar to that one in the Rrajigar Mines and the secret Skaarj base in Sky Town as some kind of isolation to keep the air inside the mothership when it's in space or something... I don't know, could be anything. Even developers don't spend much time thinking about such stuff, usually it's the fanbase which starts questioning all the things they've made. If something looks good and amazing, then they include it. Wasn't it a nice reward to see this scene with all these awesome lighting effects?
And yeah, I like to think about that stuff too! It's just too much fun.
