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At the airport Cole meets Jose who gives him a gun and instructs him to kill Dr. Peters. Now the question is - why? They make it clear in the film that the past cannot be altered and that is why he was sent to get a sample of the virus and not stop it.

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Related: movies.stackexchange.com/questions/871/… – ghoppe Sep 17 '12 at 22:25
Does no one wonder how Cole, as a child in airport , survived to grow old and become the time traveler, given he was at ground zero of the initial outbreak. – Buddy Story May 12 at 5:57
@Buddy Story: AFAIR this airport was not ground zero, the virus-spreader just took off from there to spread the virus over airports in the whole world. – atticae May 12 at 14:24
@atticae, young Cole was indeed at the airport when the redheaded scientist opened the first virus vial at the baggage check. The movie does not explain why young Cole was not infected. I've always assumed he (and other survivors) were spared just by randomness -- perhaps some sort of mutation that made them immune, or perhaps they just got lucky and didn't inhale the same toxic air particles that claimed others around them. – Shane Finneran May 12 at 21:17

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The scientists use Jose to force Cole into trying to kill the virus-spreader because they needed to learn the virus-spreader's identity.

Remember, the scientists knew Cole was at the airport because Cole had left a voicemail from there. But in the voicemail, while Cole said the Army of the 12 Monkeys did not spread the virus, he didn't say who the real culprit was.

So Jose's task at airport is to give Cole the gun and then watch who Cole goes after. But while Jose and Cole are talking, Catherine runs up and says she's figured out it is the redhead assistant to Dr Goynes who spreads the virus. At this point, Jose fades out of the scene, having got what he needed. (for confirmation see scene as written in production draft of script)

Of course, airport security shoots Cole when Cole points the gun at the virus-spreader. The scientists may have provided Cole a non-working gun to encourage this outcome.

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It's been a while since i've seen it, but I'm pretty sure the scientists from the future did not know Dr. Peters was carrying the virus. As explained on the movie FAQ at IMDB.com:

It is strongly implied that the scientists from the future planned Cole's death because he refused to return to his own time, and they could not allow him to disturb the past any further. They send Jose (Jon Seda) through time to give Cole an ancient gun and instructions to complete his mission. They might have intended that Cole try to use the gun in a(n) (futile) attempt to kill the carrier of the virus.The scientists probably knew it would not work and would cause security personnel to neutralize him, while the female scientist herself made sure the mission was completed.

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