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In Spider-Man: Homecoming,

There is a scene in which two of Adrian Toomes' men show up at Peter Parker's school to look for a Chitauri weapon that their sensors had isolated in the science lab in which Peter and Ned had just been working with the weapon. Peter returned to the lab while the men were in the lab searching. And Ned was in the same building.

Both Peter and Ned were accounted for in the same building.

So where was the weapon hidden at that time? And why couldn't the men find its hiding place with the same instruments that had isolated it to the science lab?

At that point, Peter and Ned were referring to the weapon as "the glowy thing", and it could not have been far away.

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    IIRC, the men said something about their sensors detecting that the weapon had been activated in the lab, or something to that effect. I don't think they could constantly track it, but they detected when Peter and Ned fooled around with it earlier, and were coming to investigate. Ned would still have it on him, then. Commented Jul 20, 2017 at 3:03

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The only thing that Toomes's men were looking for was the Chitauri power core, which Peter had removed from the weapon. This is the part that Ned suggested they "take to the lab" to run more tests on. Most likely the part was in the same place it would be for the rest of the movie -- Ned's backpack.

What Toomes's men were tracking wasn't the power core itself. They were tracking the "residue" that was left behind when Peter accidentally set it off. They couldn't follow the core in real-time, only when it had been "fired".

It's never shown what happened to the remainder of the weapon, but Ned points out that the other parts are pretty normal stuff, so it's possible they just dismantled it and left it as scrap in the shop classroom. Since those pieces didn't give off the same kind of "alien residue" that the detector was scanning for, they wouldn't have registered for Toomes's men to find.

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    Sounds right, as the detector seemed to be nothing more than a geiger counter.
    – Möoz
    Commented Jul 24, 2017 at 1:11

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