In XCOM 2, the storyline requires the player to

Skulljack an Advent officer. This triggers what is (at that stage in the game) a difficult fight.

The option remains to do this to other enemies, and indeed there's an achievement for doing it to every type of enemy. What is the benefit of doing this?

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    I haven't played this far yet but jamming things into ADVENT and Alien brains is always a good idea. – Studoku- Reinstate Monica Feb 7 '16 at 13:15

Before you can Skulljack for non-plot reasons you first need to research "Skullmine" in the proving grounds. It only works on the Advent trooper family of enemies, not on pure-breed aliens.

Successfully hitting an enemy in melee with the skulljack gives you a hacking attempt with a small reward of a small supply bonus and a large reward of a lead on an alien facility. Failing the hack deals 3-4 damage to the x-com operative. The success chance of non-specialists is very low, so you should leave skulljacking to the specialist class.

As a secondary benefit, a skulljack-hit is always an instant kill, even when the hacking is failed. So sometimes you might want to do one simply for tactical reasons.

The "special security feature" which you encountered during your first hack into the advent network will not bother you during non-story-relevant skulljacks.

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    Does this always spawn a codex? – Philip Pittle Feb 8 '16 at 9:55
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    @PhilipPittle no, the codex spawn event only happens on the first skulljack. – Philipp Feb 8 '16 at 13:13
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    @peper757: Imagine the awkwardness in trying to undo it, walk back to your position, and instead take a shot at the ADVENT officer who is now already screaming and in agony. – Flater Feb 9 '16 at 12:01
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    @Philipp ah, thanks! That's what's been putting me off trying again... – Flyto Feb 9 '16 at 13:00
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    @SimonW: Oh, just you wait for the second skulljack. Skullmining doesn't have any nasty surprises in store, though. – user2357112 supports Monica Feb 12 '16 at 23:42

An extra benefit is that if you've researched Skullmining, equipping the Skulljack gives your Specialist a straight +20 to hacking skill. Handy for getting those large rewards!

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    This is not a benefit of the act of skulljacking, but rather a secondary effect of the tool used to do it. You can get that bonus without using the skullmining ability at all. – Philipp Feb 10 '16 at 13:29

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