In the game, Ragna had only asked Rachel for advice in order to save Noel. But in the episode, Kokonoe also takes part in the conversation.
In the game, only Ragna had fought against Mu -No. 12-, however in the episode, both Ragna and Jin fight against Mu -No. 12-.
In the game, Lambda did not make an appearance as a spirit during the battle between Ragna and Mu -No. 12-, when Ragna uses his Idea Engine against Mu -No. 12-.
In the game, only Terumi's ghost form had appeared when he infiltrated into the Takamagahara System, but in the episode, when Phantom's virus is used against it, Phantom herself actually appears to use the virus.
In the game, Ragna inverted the Idea Engine connection towards μ-No.12 as it glows in a blue light causing his left arm to sacrifice in a crack fashion. In the anime, his Idea Engine glows in pale blue instead of blue in the game while he inverted his connection towards μ-No.12 while the latter tries to remember Noel of her past as his left arm quickly dissipates in a yellow light.
In the game, Noel cries remorsefully towards Ragna after the latter sacrifices his left arm to save her and calls him an idiot several times while he was on the ground. In the episode however, Ragna appears to smile calmly while his left arm is sacrificed to save Noel as the latter saw this and annoyingly cries towards him while pounding him on the chest and calls him an idiot.
In the game, Noel did not sense any pain after seeing the Emperor. However, in the episode, after she sees the Emperor, she feels some sort of pain.
In the game, Ragna becomes more emotional after he finds out that Saya is the Emperor, however in the episode, he is barely emotional about this fact.
In the game, Jin tells Ragna who had given him the Yukianesa. However none of this is mentioned in the episode.
In the game, Noel had given her farewell towards Jūbei and had left with Makoto and Iron Tager. However, in the episode, she wakes up in a room on a bed, where Makoto who is bandaged comes in to greet her.