Konoko
 
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Stages
Rogue agent
When Shinatama is kidnapped from the TCTF HQ, Konoko decides to go after her.
- Konoko: Don't worry Shinatama. I'm on my way.
... says she right after defeating Barabas.
Yet Commander Griffin is strongly opposed to her initiative :
- Konoko: I'm going after her.
- Griffin: I have dispatched a Strike Team to recover the SLD.
- Konoko: This is personal.
- Griffin: Which is precisely why you should have nothing to do with it.
- Konoko: My mind is made up.
- Griffin: I am your Commanding Officer...
- Konoko: I don't care who you are. My friend is in trouble and I'm going to help her if I can. Stay out of my way.
Disobeying a direct order from her commanding officer already qualifies Konoko as a rogue agent at the beginning of CHAPTER 07 . A FRIEND IN NEED.
OK, we don't see a direct order in that dialogue, but the "I don't care who you are" is a case of major insubordination in any book.
So, technically speaking, Mai is not on a mission in CHAPTER 07 . A FRIEND IN NEED and CHAPTER 08 . AN INNOCENT LIFE : as good as not affiliated with the TCTF at all. She's on her own.
Which is one of the reasons why she could have chosen to wear another kind of gear than what she wore on her missions until then : Black Ops gear ^^
Other reasons are :
- The first missions are carried out by day. Going after Shinatama means night-time infiltration. Black Ops gear is good for that.
- Konoko is (plotwise) seconded by a TCTF team on her first missions, so a clearly identifiable TCTF label can prevent friendly fire etc. None of that here.
- Getting out the coolest toys when it comes to saving her best an only friend would make sense. Imagine a cutscene when she straps that stuff on... ^^
Mai Hasegawa
Loquacious Shinatama
CHAPTER 08 . AN INNOCENT LIFE is where Konoko first learns her real name. It is spoken by Shinatama, but at that moment Konoko ignores almost everything Shinatama tells her.
The CD
CHAPTER 11 . DREAM DIVER is where Konoko learns most of the stuff about her parents : Jamie Kerr and Professor Hasegawa (first name unknown). She and her brother (Muro) are not referred to at all in Hasegawa's diary, except for the newspaper article GRAD STUDENT DIES : MURDER OR MERCY : "Jamie Kerr Hasegawa, environmental activist, top grad student, mother of two".
Science Prison
Konoko is referred to as "Hasegawa, Mai" in the terminals there. The readout relates mostly to experiments performed on Mai at some undefined time.
After scanning Mai, Kerr acknowledges that Muro, Mai's archnemesis, is indeed Mai's brother. He does not, however, make any statement as for Hasegawa's fate or whereabouts.
Daodan symbiote
The fact that Konoko is not 100% human is suggested by cutscenes throughout the first part of the game. Konoko herself is of course unaware of those sequences, but the sequences supply too little information for the player to know much more than the character.
Filling in...