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I am aware of this question (I anticipate people linking it to this one in less than 3 seconds since I hit "Post"), and I am asking something more precise and somehow different.

When some enemy force boards the ship, why doesn't a program run in the computer that just performs the following task: while there is energy available and the transporter is up and running, every member of the enemy force is transported to a precise location. No need to be violent: let's transport them to a dedicated brig, their weapons disintegrated. I imagine the Cardassians or the Dominion tweaking the program to beam the enemies 10 meters outside the hull.

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    Because plot cannot happen then. I do not believe there is an in-canon answer, other than that didn't work the one time it was actually tried. – Tritium21 Nov 13 '14 at 0:34
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    typically i assume if they were able to bypass the shields and enter the ship, they either have disabled enough of the ship to stop transporters working, OR have some sort of device that blocks teleporation, i assume this would be a simple sheilding device that simple makes it so your unable to be teleported unless you have X frequency (to allow you to be beamed back to your ship. – Himarm Nov 13 '14 at 0:34
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    something as simple as the combadge could block the transporter, like i said its not actual Sheilding, more of a disrupter of the locking on sensors of the transporters. just a simple single broadcasted blocking the teleporter. for locking on them. – Himarm Nov 13 '14 at 0:40
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    All of this makes sense: why don't you post your comments as answers? Anyway I believe the whole "board the ship" thing is flawed from many points of view. Just to start: if the enemy is resilient to the transporter beam and yet vulnerable to phasers, let's install an automatic turret in every room. Automatic tracking and aiming, self-powered, n times the firepower of a standard issue phaser (you pick n), job done. I find this old fashioned military procedure incompatible with that great deal of technology they have. – gd1 Nov 13 '14 at 0:43
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    basicly it comes down to this, in federation ships at least, they are peaceful, if some new alien teleported in without asking, got shot and or put into the brig as the first responce, it wouldnt be very peaceful. klingons wouldnt do this either as it wouldnt be honorable, they woudl rather have a bloody brawl. – Himarm Nov 13 '14 at 1:00
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Transporting enemies direct to the brig and rendering them weaponless is a sound idea. But there are several means of preventing such a thing from taking place including a technology common to the Alpha Quadrant: The transport inhibitor.

  • A transport inhibitor was a device that blocked transporters attempting to dematerialize objects in a specific area.

  • In 2375, Lieutenant Commander Data used a transport inhibitor aboard the Federation mission scoutship to prevent himself from being beamed away by an USS Enterprise-E shuttlecraft. Several portable transport inhibitors were later deployed by Enterprise-E personnel on the surface of Ba'ku to prevent the Son'a from forcibly removing the inhabitants of the Ba'ku village. Due to their large size and easily noticeable positions, several were destroyed by Son'a shuttles. (Star Trek: Insurrection)

Depending on the species, transporters particularly during ENT and TOS had so many limitations, they were fortunate they worked more often than not. In the TOS era, movement wasn't even possible while transporting until late in the century.

  • The transporter is vulnerable to a number of different materials and electromagnetic fields beyond the shields. A person boarding a ship could use an inhibitor or utilize a personal shield which could emit a transporter scrambling field, since strong magnetic fields can make the transporter balk at an unsafe transport.

  • Certain minerals could also perform the same effect. A boarding party could be beamed to a ship with scrambling materials in a shielded container. Upon arrival, they put on the scrambling material until they have completed their mission. When they are done, they drop the scrambling mineral on the deck and beam away.

  • Transporting enemies to the brig has another snag. During red alert particularly in the Next Generation era, there were force fields able to be placed inside the ship preventing loss of atmosphere and preventing movement through the ship. These same shields would also prevent transporters from working. Granted, their shield frequencies would be known to the crew but making them a standard frequency might make it possible for a spy to learn that frequency and then beam directly into sensitive regions of the ship. It is these barriers which prevent such deep ship beaming as long as there is impulse or warp power available.

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Limitations and one of those things that needs the human touch really. Voyager transporters however could probably perform this action as they can isolate biomaterial that doesn't belong such as viruses from subjects being transported. I also believe during this time transporters could also remove weapons from those beaming in, so long as they're using the host transporters and not their own.

That aside, as it is made known throughout Star Trek that technological errors occur. It be mildly inconvenient if someone tricked the computer into thinking its own crew were intruders and transporting them to a place setup for confinement. Just think, Siska would have had it a lot easier if she were able to utilize Voyager's transporters in this fashion. Plus, what if several bio-neural gel packs were damaged and started beaming people to the brig for seemingly no reason? Just imagine the bridge crew being transported to the brig during a battle. So it makes perfect sense to just give the bridge crew an alert that something or someone doesn't belong and let them decide how to handle it.

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