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01. Awakening
02. Sinking of a Ship
03. Encounter
04. Place of Death
05. Anomoly
06. Betrayed
07. Encephalon
08. Memories
09. Song of Nephilim
10. Weapon
11. Inside
12. KOS-MOS
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Awakening - Episode I

Spoilers! This covers almost every aspect of the Episode. Do not read if you do not want to be spoiled!
After the theme song scenes, the episode opens with Shion Uzuki in an Encephalon Dive testing out KOS-MOS's battle capabilities. All goes well until one of the AIs aim for Shion. She is then saved in the nick of time by KOS-MOS. Afterwards, Allen ends the dive with Shion's approval.
As Shion comes out of the dive, she falls into Allen's hands. She admits that she was a little shaken up by the experience, but wanted to see KOS-MOS's abilities with her own eyes. After a bit of talking, Allen reminds Shion that she needs to report to the Bridge with her data, and that he would take care of cleaning up from the last test run. He also asks Shion to rest after she finishes her report. After Shion leaves, the other workers of 1st Division pick at Allen and say that Shion really "has him trained". A recent addition to 1st Division then asks Allen why everyone is being so cautious. Allen explains that they're being careful after the previous start up incident while all the other workers are rather silent.
The scene then moves to the hangar that stores the Zohar Emulator. The head of the block lectures his workers while they complete tons of push-ups. As this occurs, Shion walks into the room and notices the Zohar Emulator. One of the workers then brings up a key question. If their main purpose was to invistigate the disappearance of the Planet Ariande, why did they need to go through so much trouble to get the Emulator? When Shion walks over to the Zohar, time itself seemed to freeze, and a mysterious girl appeared in front of the golden object. Shion asks for her name and reaches out, but is rudely awakened by the head of the block. She is then lectured before being forced to move on.
The scene then moves on to a mysterious man lecturing Andrew Cherenkov. The two discuss the incident involved when retriving the Zohar Emulator. When the scene ends, Cherenkov reveals that the man he was speaking to was indeed named Margulis.
The scene then moves to the Bridge of the Woglinde. Shion had just finished giving her report to the head when Andrew comes in and examines the data. As this happens, Shion looks around and notices a 100-Series realian. Their eyes meet and they have a calm moment which is interrupted by Andrew Chenkov. He bashes on Shion for not having any field data of KOS-MOS. Shion tries to tell him of the risks of rushing the project, but Cherenkov retorts by explaining the Gnosis danger that humanity faces. The commander of the fleet then tells Cherenkov to give Shion a break because they already have so many other helpful innovations(ex. AGWS, Realians). As this occurs, the 100-Series Realian Shion had met eyes with left the scene.
The episode then moves to hyperspace to show the Gnosis approaching the fleet that the crew is in and moves to "commercial" in a sort.

When the episode comes back, Shion is back in her room talking with her brother. The scene shows that Shion still does have her squabbals. As she tries to sleep, Shion flashes through everything that happened through the day. She then wakes up and goes to the Realian room. Apparently, they were having "issues" and needed a professional to help out. Shion then helps to explain some of the issues the realians are having and fixes the problems a bit. As she does this, Shion admits she actually wants to work in the 3rd Division which is involved with Realians instead of Software Development (1st Divison). Shion then realizes that the 100-Series Realian she saw earlier was in the same room.
When Shion approaches her, the Realian starts out by not responding too much to what Shion says. To help foster their realtionship, Shion gives the Realian a charm and helps to counsel her.
After bonding, Lieutenent Virgil comes into the room and begins to make fun of the Realians. The 100-series realian Shion had talked to was scared, so she grabbed onto Shion's hand during the time. Shion then stands up for all the realians and Virgil argues back by retorting that Realians are equipment to people in Vector like Shion. Another Realian then stands up for himself by telling Virgil that he has his own "free will", which helps the 100-Series overcome her dillema and cuases Virgil to leave.
The emergency siren is then sounded to indicate the Gnosis are approaching the fleet. Soon later the Gnosis appear and begin attacking the fleet. Thus, the fleet deploys all AGWS and realians. Thus, the 100-Series ran off to get to her position with Shion following. After a short battle sequence occurs, the Gnosis break through into the ship. Far off in the distance, a man in a machine makes a few remarks.
The scene then moves to Allen in 1st Division who is trying to contact Shion. He then tells the rest of the Divion to get out. The scene then changes to show a Gnosis attacking a couple and many other crew members. Fighting then occurs inside the Woglinde.
Shion and the Realian then hurry and move toward KOS-MOS's place. The realian falls, but is picked back up by Shion. However, the ceiling collapses and the Realian pushes Shion out of the way to keep her from harm. When Shion hits the wall, KOS-MOS awakens. Shion then loses consciousness when seeing a giant robot in front of her. A shocked Allen then see KOS-MOS awakening and searching for Shion. As KOS-MOS makes her entrance the Episode then ends by recapping how Allen, KOS-MOS, and Shion are doing.