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KOS-MOS, the final episode of the series, is the only episode title written in romaji (English letters).
Even though the story of the series was changed drastically from the story of the game, the ending was left fairly intact. The only major differences are the presence of the Blue and Black Testaments with Wilhelm (originally, it was only Red, and Black was not even revealed until the second game), the presence of Canaan with Helmer (Canaan was also not introduced until the second game), the lack of scenes of Nephilim and Abel, and the change in location of Shion and KOS-MOS' reunion (originally, chaos brought KOS-MOS to the restaurant where everyone was waiting)
Pellegri's dive while piloting the ES Issachar implies that the ES units are equiped with dive equipment. However, this was not realized in the games until Episode III.
Even though it's an adaptation of the first game, this episode reminds us that the anime was made after the second game was released (or at least was being made simultaneously, but the 2nd game was released first). There are a few things in this episode that are from Episode II. The first is chaos and Jin's conversation, which is partially from Episode II, but the knowledge that they knew each other previously was not known until Episode II (in fact, Jin only appears in one scene in all of the first game). The second is ES Issachar, Pellegri's mech. The first time you see ES Issachar in the games is the opening scenes of Episode II. The third is chaos and Jin's use of "Hyoumon Ken" ("Ice-Gate Sword", or "Ice Brand" in the US version), their dual-tech from Episode II. The final instance is actually behind the scenes in Episode II, which is chaos and Jin's unspoken agreement to act as if they don't know each other when they meet up later.
The attacks used in this episode are Storm Waltz (Jr.), Mystic Nocturne (Jr.), Meteor Shot (Ziggy), Lionel Hand (Ziggy), Last Symphony (Jr.), Starlight Dress Up (MOMO), Queen Kiss (Shion). Note that Queen Kiss and Starlight Dress UP are actually Ether spells originally, not attacks.
"Encephalon" is the only episode of the series written in katakana (which is generally used for borrowed and non-native Japanese words), and one of only two episodes not written in kanji (KOS-MOS is the other).
Hikaru Midorikawa, voice of Wilhelm, doesn't play Wilhelm in the games (that role belongs to Nobuyuki Hiyama). However, Midorikawa does get a role in Episode III.
The Hilbert Effect generates a realm that intersects the imaginary space with the real space allowing the Gnosis to be killed without waiting for them to appear in real space.
The 100-Series Realian is a fake according to Albedo.
KOS-MOS did not throw Lieutenant Virgil down the shaft like Shion and Allen because he is not apart of the Vector crew.
Shion's lover was killed in the earlier testings of the KOS-MOS archetype.
Humanity abandoned earth 4000 years ago.