The Lieutenant or Lou, also lovingly dubbed Lou Tenant by some of the Super Mutants, is the Master's right hand and the overseer of all work inside the Military Base. Lou is a good example of how the Master would want his mutants to turn out, more intelligent, stronger and generally better than normal humans.
The Lieutenant's origins are shrouded in mystery as not much is known about his life prior to his transformation. However, after his transformation into a Super Mutant, he quickly became the Master's favorite creation due to his high intelligence and devotion to the Master's vision. Among other Super Mutant commanders who led the Master's army, the Lieutenant was appointed to the highest position, being the overseer of the Mariposa Military Base and supreme commander of mutant operations in the surrounding region.
The Lou's authority apparently stretches so far that Harry goes through the trouble of dragging the Vault Dweller on a long journey through the Wasteland just to show him to the Lou and report he is not a ghoul. Other than the Master himself, Lou is the best source of information about details concerning the Vaults, Super Mutants, and the general grand plan of Unity. He appears to be a rather sadistic character who thoroughly enjoys torturing the PC, as well as arrogantly self-assured concerning the superiority of Super Mutants over normal humans and Ghouls, referring to them as the "next step in human evolution".
During the Vault Dweller's quest to stop the Master and destroy the VATs, the Lieutenant resided on the fourth sub-level of the Mariposa Military Base. Here, the Lieutenant would interrogate the Vault Dweller, in hopes of gaining the location of Vault 13. In the end, the Vault Dweller successfully destroyed the Mariposa Military Base and with it the source of the super mutants. During this operation, the player could chose whether or not to visit Lou (thus dooming him to be killed by the explosion), or engage him in battle, and kill him.
The Lieutenant is noticeably tougher and smarter than standard Super Mutant soldiers. He has about 250 to 300 hit points, and is equipped with a Gatling Laser. He has several cybernetic augmentations (including a bionic eye), and also appears to be wearing metal armor custom-made for his Super Mutant bulk. During the battle, he is aided by VanHagan and two heavily armed Super Mutant commanders (plus, some brainbots could intervene and strike the player from behind). He has a unique death animation in which his body literally falls apart, resulting in quite a painful death.
The Lieutenant's death animation and overall appearance suggest him being further upgraded by the Master after his initial transformation. His metal armor and implants probably act as life support, because after him losing all the hit points, the head implant breaks, triggering his stomach and knees to blow up from the inside and his arms to slowly melt away. Probably, Lou was, in fact, less affected by FEV that other mutants, so the Master decided to make FEV run through his body permanently. That's why after the damage, Lou's body started to fall apart, rejecting it's current state.
The Lieutenant of the Mutant Army appears only in the first Fallout.