The Super Mutant is the next advancement in human evolution. To save the world, we will convert all the worthy individuals. Simple, efficient, glorious.
The Lieutenant or Lou (also dubbed Lou Tenant by some of his subordinates) is the Master's right hand super mutant and the overseer of all work inside the Mariposa Military Base. Lou is a good example of how the Master would want all his mutants to turn out: more intelligent, stronger and overall superior to normal humans.
Think of an urbane and well-educated college professor who has become the very essence of evil incarnate. He is highly intelligent, and is second-in-command to the Master himself. He genuinely believes that the super-mutants and the Unity are the future of the planet, and will do anything to see them succeed. Humans, from his point of view, are less than insects, good only for the Vats, or for being crushed.
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. It may have something to do with him being free from radiation, indicating that he may have come from a Vault. 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.
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 Lou and report that he is not a ghoul. Aside from the Master himself, Lou is the best source of information about the Vaults, super mutants, and the general grand plan of Unity. He is a rather sadistic character who thoroughly enjoys torture, as well as arrogantly self-assured concerning the superiority of Super Mutants over normal humans and ghouls, referring to the former 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 Dweller could choose 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 HP, 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 Van Hagan and two heavily armed super mutant commanders (plus, some brain bots that can intervene and strike the Vault Dweller from behind).
The Unity is the goal of all Super Mutants. Through the FEV virus, we will bring all of humanity together in peace.
The FEV virus was discovered by the Master many years ago. It is what makes us the Chosen Ones. But you will soon learn that, I assure you.
The Master is father to us all.
Nothing but a device to further our plans. No matter, all humans will be Chosen...or dead.
The Vats are where the FEV is stored, and where you normals become one of us. Of course, some die horrible, excruciatingly painful deaths, but well, those are the breaks.
They are humans who have not been exposed to radiation. They tend to fare better in the Vats than others. You are a perfect example of this.
They were constructed before the war. They are also our main source of Prime Normals.
Morpheus. It's quite amusing. He thinks he's so much more than just a slug the Master recruited to head his Children of the Cathedral nonsense. Ah, well. He, too, will be dipped in the Vats and he'll probably die a horrible death...I hope.
He has a unique death animation in which his body literally falls apart, resulting in quite a gruesome demise. His 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 he dies, the head implant breaks, triggering his stomach and knees to blow up from the inside and his arms to slowly melt away.
A subtle reference to "Lou Tenant" is made in Fallout: New Vegas during the quest G.I. Blues. When the Courier talks to Wayne about being attacked, he will mention that one of them was called Lou, and on further thought, Lou Tenant. He will then be corrected by his friend Roy, who says he means "Lieutenant," and that Wayne can be "dumber than a mutant."
During the interrogation, there's a possibility to give in to the torture and reveal the location of Vault 13. This will result in a cut scene, where the Vault Dweller is dipped into a tank of FEV while Vault 13 is being raided by Super Mutants, after which the game jumps back to the main menu. This can be considered a possible non-canonical ending.