Men in Black
Karl Haushofer and Lin Sui-Xi work for the above "Boss" in tracking down and assassinating most of the Knights of the Eastern Calculus. They are not told the true plan, but they know that Eiri Masami is involved. They say that they "don't need a Wired God".
The Men in Black make their first appearance in Layer 02 in which Karl conspicuously watches Lain from behind a lamp post, notably without his eyepiece. They re-appear in Layer 03 in front of the Iwakura residence just as Iwakura Mika has returned, much to her confusion and anger. In response to Mika's threat that she would call the police, Karl and Lin tell her that she had never seen them, nor had they ever been there.
In Layer 04 the Men in Black show up once again at the Iwakura residence, this time at the climax of Lain's fevered activity on the Wired. Angered by their intrusion, Lain yells at them to "go away" and causes Lin's eyepiece to malfunction, wounding him as well. This causes both of the agents to flee.
They are noticeably absent from Layer 05, returning in Layer 06 to confront Lain in person. She accuses them of being part of the Knights, but Karl simply tells her to "get down". Seconds later her coolant system explodes, shattering her window. Lain accuses the Men in Black of the act but Karl tells her that they planted a parasite bomb in her coolant system. Lain is still not convinced that the Men in Black are innocent, and Karl states again that it was the work of the Knights. The Men in Black depart, leaving Lain speechless and shocked.
In the next layer they intercept Lain as she returns from class. They request that she come with them, and promises that they do not intend to harm her. They escort her to the Boss, witnessing Lain's shift in identity in the process when she is mercilessly questioned. As the more assertive Lain persona excuses herself, Karl tells her that she "is what is dangerous". The boss tells the Men in Black that something interesting is taking place, and that the three of them should observe the events to come.
The Men in Black do not resurface until Layer 10, in which the identity of the Knights are released worldwide by Lain. The pair assassinate Takuyoshi Masuoka, injecting a lethal substance into his neck. Subsequently, a mass suicide of the Knights takes place.
In Layer 12, Karl suspects that they have been betrayed by their employer due to his contact with Masami Eiri. He also believes that Eiri still lives despite his supposed suicide, to the bewilderment of his partner. Moments later, they are approached by their Boss, who confirms Karl's suspicions. Karl recounts that they had been told to escape -- the boss says smugly that it should be somewhere "...where there is no electric wires and no electromagnetic waves from satellites.” Lin responds with outrage, saying that there is no such place on earth. Karl asks his erstwhile client what will happen when the real world merges with the Wired without devices. The boss simply replies that something "wonderful" will happen, and that he is looking forward to it. When he leaves, Lin is suddenly stricken with inexplicable pain and begins screaming in fear. He then collapses and begins convulsing, his body contorting wildly. Karl rushes to his aid, shocked to find an image of Lain in Lin's retina. He then realizes that his partner is dead. Moments later Karl is stricken by a similar terror and anxiously scans his surroundings before being confronted by a shadowy image. Karl lets out a similar horrified scream as the visage closes in, perhaps meeting the fate of his partner.