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I forgot to post the GDI version of this, so here you go; and a quick explanation of hacking:
In Renegade, an Engineer loudly rolled up to a building, perhaps had a buddy suicide through the proximity C4 in the doorway, then threw his C4 on the MCT and hoped for the best. Either he did significant damage to the structure (or outright killed it), or accomplished nothing at all aside from giving the enemy some cash and points for disarming his C4.
Here, Engineers are encouraged to sneak up to buildings-- perhaps under the cover of an attack on another part of the base-- and begin silently hacking their target structure.
The results of this sabotage vary based on the target; you could knock out base repairs, shut down all the base defenses in preparation for an airstrike, disable the Ion Cannon or Hunter Seeker uplinks, and even prevent the enemy from purchasing any assault troopers more sophisticated than Riflemen. Sabotage is *not* permanent unless you stick with it for a while, but it is faster than simply pounding a building with artillery, and it gives the enemy very little warning.
Engineers are free to sneak between buildings, nearly-hacking several before pulling them all down at once. Or perhaps the Engineer wants to try cutting power to the Obelisk before dashing for the Tech Center. Or of course, reinforce his hack on the main target-- *permanently* disabling it given enough time.
Structures not permanently disabled will slowly unhack themselves, but there's no efficient way to "undo" the hacking damage; it is immediate, it adds up over time as other Engineers follow up on the first attempt, and with enough time you can permanently disable a structure.
By the way, those Engineers back at base can level up their skills while repairing friendly buildings; and don't bet on a veteran or elite Engineer showing up on radar as he approaches your base.