Adaptation Displacement: Even though the visual novel and OVA received releases in the United States, Requiem for the Phantom is the most popular version of the story. This is a result of the fact that the visual novel is very rare to find a copy of and the OVA only adapted the first act of the story. The OVA at this point seems to have been widely forgotten.
In Requiem for the Phantom the third act of the story was very divided among viewers. Either you like it for being a climatic way of wrapping up the story with many intense and tearjerking battles, or dislike it for shifting the setting to that of a Japanese high school and the last few episodes killing off a majority of the main characters.
The ending to Requiem for the Phantom has had divided interpretations. For some Zwei's ambiguous death was effective as he had nothing else to live for and as an assassin his past would eventually catch up to him. However for others the fact that it occurred right as the anime adaptation was about to end and he had already been through enough suffering made it feel forced.
Visual Novel & Phantom: Requiem for the Phantom anime: Dr. Helmut von Giuseppe, better known as Scythe Master, is a sociopathic neuroscientist who brainwashes people he sees potential in to becoming the perfect assassins. Kidnapping one such individual, Reiji Azuma, Scythe erases his memories, renaming him Zwei and having another of his assassins, Ein, whose memory he also wiped, train him before sending the duo off on countless missions to kill enemies of his organization, Inferno. When Reiji and Ein escape from his clutches, Scythe turns to Reiji's young friend, Cal, corrupting the young girl into hating Reiji and becoming his psychotic killer. Using Cal on many missions, Scythe even sends her after his own friend, who had sheltered him when he was framed for betraying Inferno. Deeming the three assassins prototypes, Scythe creates a new batch of emotionless killers and sends them after the trio, watching the combat with delight.
Phantom: The Animation OVA: Scythe Master is a greedy scientist willing to do anything to fund his depraved research. Creating assassins for the criminal syndicate Inferno, he has them carry out violent hits to prove their effectiveness. Deciding a rival of Inferno would better fund him, Scythe betrays Inferno, having his prized assassin kill everyone in his laboratory while fleeing. When Inferno hunts him down, Scythe has the two assassins he created, Ein and Zwei, fight each other while he activates bombs in the building, even with his own men still inside.
Darkness-Induced Audience Apathy: Being written by Gen Urobuchi this one is a given. Being one of his earliest works it is one of the darkest narratives he has ever worked on. There's hardly any comic relief, and there is always a sense of omnipresent danger. Taken Up to Eleven in Requiem for the Phantom which adapted the most depressing route of the visual novel which involves a majority of the cast being killed off.
Older Than They Think: The style of the masks Scythe's assassins wear in the anime caused many fans of Darker Than Black to notice similarities to mask series protagonist Hei wears, making them believe that the Phantom was copying that show's style, even though the visual novel predates Darker Than Black by 7 years.
Replacement Scrappy: The first opening theme Karma is a foreboding song that does a great job at building atmosphere for the series and unlike other anime opening themes it plays for 19 episodes instead of 12-13 like most two-cour series. Needless to say replacing it with a more upbeat ALI Project song in the second half did not go well with fans.
The Scrappy: Mio Fujieda especially because she plays an important role in the very divisive third act of the story. While Ein and Cal had interesting backstories and relationships with Zwei, Mio is just a normal schoolgirl that suddenly appears in the plot. The fact that her most important role in the story is getting kidnapped by Cal and having to be rescued by Zwei didn't really help her either. However some were relieved to see that she was one of the few characters to survive the plot and have a happy ending in Requiem for the Phantom.