In the premise of the story, a newly evolved species of humans, called "Diclonius", came to the world. Notable traits that distinguish "Diclonius" from normal humans are pink hair, horns protruding from the skull, and an invisible set of hands named "vectors", which is able to rip through flesh and material with ease. Due to their tendency to murder humans wherever they roam, the government orders the extermination of the Diclonius and any surviving members of the species caught are experimented in a secret facility. One of these subjects, codenamed "Lucy", stage a bloody escape from the facility, killing everyone in her way except Chief Kurama. Before making her escape, she was hit by a glancing sniper bullet to the head and falls to the sea. The protagonist Kouta and his cousin Yuka found her while walking along the beach, however "Lucy" appears to them in a childlike state, an effect from the bullet hitting her head during her escape. Kouta and Yuka takes her in to their house and named her "Nyuu" for the only word she is able to say. While they tend to "Nyuu", the government begins responding to the escape with the National Police Agency's S.A.T. to apprehend and terminate "Lucy". The story follows as the Kouta and Yuka gets involved with many incidents the government creates to find and capture "Lucy".
The following weapons are seen in the anime series Elfen Lied:
Kakuzawa, the head of the Diclonius Research Facility, uses a stainless-steel SIG-Sauer P220.
SIG-Sauer P226
The sidearm for police officers and S.A.T. forces, most noticeable scene is when Bandou, while shipping out to locate "Lucy", talks down one of his squad mates with a stainless steel SIG-Sauer P226. Police officers apprehending Lucy when she was a child are armed with P226 as well
Desert Eagle Mark XIX
In a rare case of justified use of a Desert Eagle, the mercenary Bandou wields two of these .50AE handguns against any Diclonius (One is kept as a backup weapon). He says the pistols are loaded with "custom .50 Tungsten rounds", which can passes through the Diclonius vectors as opposed to normal pistol rounds due to its mass and velocity, making this normally ludicrous weapon choice perfectly reasonable.
M1911 pistol series
A pistol from the M1911 pistol series is used by Chief Kurama in the final episode.
Unknown Snub-Nosed Revolvers
Used by a security guard in the first episode and in episode 10.
Sub-Machine Guns
Heckler & Koch MP5
Both Japanese S.A.T officers and security guards inside the Diclonius research facility uses the A4 and A5 variants of the H&K MP5 sub-machine guns, given that all have a Safe/Semi/Burst/Auto selector option. This is by far most seen weapon in the anime.
MP5A4
MP5A5
MP5A5 with M203 attachment
Bandou uses a unique MP5A5 outfitted with a M203 grenade launcher during his hunt for the escaped Diclonius "Lucy". Disappointingly, he only uses the grenade launcher once despite his MP5 9mm rounds failing to damage Lucy.
Rifles
FAMAS G2
Professor Kakazawa uses a FAMAS G2 in episode 10 to kill a loose Diclonius, stating that while the Diclonius' vectors can block normal bullets such as the MP5 9mm rounds, it can't stop an armor-piercing round such as the 5.56 so easily. Which begs to question if this logic was discovered early, why is the security armory only filled with MP5s?
AW50F
A AW50F is used by a guard against Lucy in a last-ditch attempt to thwart her escape.