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Engineers were trained to capture and repair buildings in case of emergency.
Engineers have two purposes:
1. To capture enemy structures. When ordered to enter an enemy building, the engineer will instantly take control of it.
2. To repair own buildings. The engineer can bring a building instantly to full health. The unit disappears in the process, however.
While an transport vehicle full of Engineers are capable of capturing a small base, they are unarmed and weakly armored and must be protected by supporting infantry and vehicles, else the Engineers will be simply killed before having a chance to do their duty.
If a commander's goal is to capture the enemy base, or the remains of one, it is advisable to clear the enemy base of it's defensive structures and the garrisoning units within the base and the surrounding area, and then directing Engineers into various key buildings, such as the enemy Construction Yard, Power Plant, and/or Barracks/Hand of Nod.
If a commander's goal does not include the capture of a base, then they may instead train a small garrison of Engineers and re-locate them to a safe area away from the front lines and use them to repair badly damaged buildings instantly. However, this may prove to be costly ($500 per Engineer), inefficient due to the long training time of recruiting one Engineer (0:33 based on having one Barracks/Hand of Nod), and using up the training slot for infantry when other infantry units could be needed at the moment.
The Brotherhood of Nod in the First Tiberium War had no means to mass produce their own APCs, relying instead on capturing a GDI Weapons Factory in order to do so. The few available ground-based transports the Brotherhood of Nod had could be used to ferry Engineers from point A to point B. Commanders who could not build APCs had to rely on building a second base with another Hand of Nod, capturing an enemy Barracks to train new infantry, capturing an enemy Weapons Factory to build their own APCs, or pile Engineers into a Chinook transport helicopter if one or more is available. After the First Tiberium War, the Brotherhood of Nod started manufacturing an advanced APC that could dig under ground and transport a squad of infantry into an enemy base for a surprise attack, and follow up with another APC to re-surface and unload a squad of Engineers and capture several key structures. However, it could not re-surface under a body of water, a concrete foundation, or rough terrain. The GDI in the First Tiberium War could build as many APCs (if a Weapons Factory is up and running) and Engineers as the commander's budget would allow, and flood the enemy with squads of mechanized infantry. If a GDI Weapons Factory was not readily available, the GDI would have to resort to using similar methods and tactics of transportation that restricted the Brotherhood of Nod's use of Engineers in the First Tiberium War.
After the First Tiberium War, the GDI fazed out their first generation APCs for an amphibious APC that could carry a squad of infantry across hazardous terrain and bodies of water and into an enemy base. However, it still required an armed escort to protect the APC and it's passengers, for this version had to lose it's heavy tracks, machine gun, ammo, and some of it's armor in favor of speed and the light weight needed to be able to float in (preferably calm) bodies of water. Around this time, the Brotherhood of Nod started manufacturing an advanced APC that could dig under ground and transport a squad of infantry into an enemy base for a surprise attack, and follow up with another APC to re-surface and unload a squad of Engineers and capture several key structures. However, it could not re-surface under a body of water, a concrete foundation, or rough terrain, and required to drop off it's passengers and leave or else risk itself to enemy fire, for it has no defensive armament, relying on surprise in order to achieve success.