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In the movie Independence Day Captain Hiller (Smith) and David (Goldblum) fly an alien-ship that had been in our possession since the 1950s (explicitly mentioned more than once in the movie) into the Mothership to upload the virus, nuke the ship, and fly out of it.

When they near the alien Mothership, the smaller ship's pilot is overridden and David says something along the lines "I was counting on it".

But how is it possible that the aliens did not notice that the ship coming back was a much older one and arguably of a different make too. And, if they indeed had noticed, why did they take it in? Wouldn't a ship lost 50 years ago coming back seem suspicious?

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Considering the virus to ruin the ship was made on a Mac and uploaded to an alien computer, I think its safe to say this movie is full of holes like this :P –  TylerShads Jun 28 '13 at 13:16
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A deleted scene explains how we got all our computer tech from the original crashed ship - this is why their Mac is compatible. Not trying to defend it or anything though... :) –  Nobby Jun 28 '13 at 13:43
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VADER Do they have a code clearance? PIETT It's an older code, sir, but it checks out. I was about to clear them. Vader looks upward, as he senses Luke's presence. PIETT Shall I hold them? VADER No. Leave them to me. I will deal with them myself./ I am just showing precedent for an older ship being allowed in. i know that ROTJ isn't ID4 –  Dan Jun 28 '13 at 13:49
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Just to be a professional Star Wars nerd and nit-picker, the shuttle wouldn't have been allowed through if Vader hadn't sensed that Luke was on board. :) –  Nobby Jun 28 '13 at 14:37
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But Nobby, to nit-pick even further, didn't PIETT say "I was about to clear them"? :) –  Shiz Z. Jun 28 '13 at 16:12
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Another explaination would be that space travel would have to be at light speed or greater to make it even feasible to get anywhere in a reasonable amount of time. This is where the theory of Relativity comes into play. When traveling at light speed or above, time speeds up for non-moving objects and stays the same for those traveling at those speeds and beyond. Therefore, to the Aliens, this long lost fighter ship that comes back to them, like a Trojan Horse, may have only been gone for a short time or a fraction of the 50 years it had been left on earth for, in our observation.

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Whatever relativistic effects the mothership went through, the scout most likely took the very same route 50 years ago. But still I like this answer, the mothership might just as well have taken a 50 light years detour to "harvest" another planet first... –  Tobias Kienzler Jun 29 '13 at 7:25
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Of course a possible out-of-universe explanation is that this inconsistency was just ignored by the filmmakers (since Independence Day is not that famous for its realistic plot).

But one could also come up with some possible in-universe explanations for this:

  1. I didn't get the impression that the ship was really different from all those others, maybe they didn't change it in 50 years. Likewise they might just not have checked some kind of electronic identification number or whatever to realize that this particular ship was lost some years ago.

  2. Another possibility is, that Dan wasn't so far with the Return of the Jedi reference from his comment. Maybe they really sensed something strange going on with that ship. Which might even be the reason for the tractor beam (or why they tried to open the windows to see who's in there). So they let it in to check what was going on, or what this old ship was doing here. They just didn't anticipate the humans waging such an ingenious attack that could bring down their whole mothership (maybe out of their success-induced arrogance) and before nuking this small ship just out of fear, they wanted to know what was going on with it.

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I like your #2 reason and now regret my response to Dan in the comments. Damn you, interwebs, you win this day. –  Nobby Jun 28 '13 at 14:38
    
@Nobby "I like your #2 reason" - Then I hope you at least ignored (or maybe also liked) my #1 and #0 reasons (to net me an up-vote). ;) –  Napoleon Wilson Jun 28 '13 at 14:45
    
I've found that most of Roland Emmerich's films have plots filled with very large holes and blatant errors, but his movie flaws are often overlooked because of the FXs that make them best appreciated on the Big Screen. –  Xavier Casto Jun 28 '13 at 15:34
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@XavierCasto Might be true. Yet if one knows what to await from an Emmerich-movie and what not, they can be really enjoyable. –  Napoleon Wilson Jun 28 '13 at 16:09
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@ChristianRau Thats because if they could cover the plot hole without creating more plot holes they would have covered in in the first place. I'm sure plot holes are left as plot holes because any answer they can find to completely fill it would either be too boring, too expensive, or too cheesy ("Oh no our 72 stage defensive procedure has malfunctioned letting the ship in regardless" or "An alien switches sides because of seeing humanities passion for survival" or some other obvious filler!. Perhaps the one in charge of checking was just lazy, im sure no race is perfect! –  RhysW Jul 1 '13 at 15:25
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Advanced civilizations (space-faring) probably wouldn't feel compelled to re-design things every 5 years, (especially if their technological progression had slowed).
The aliens in Independence Day would be even less likely to do this since their whole reason for moving from planet to planet is a lack of resources, one of those mother-ships would require a lot of raw material, so a single old fighter might not raise suspicions (or even noticed).

While this doesn't address the authentication issue, the aliens could be:

  • Overworked, it was a big fleet.
  • Arrogant, so haven't taken any precautions against having their tech co-opted.
  • Expected, many fighters from that era might exist for the reasons above.
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