-In this version, we learn there are 4 elevators to IBF- 2 exclusively for researchers. Takeshi asks if they go to the surface, and while Sora says they do, both are currently broken, so only the ones between IBF and HIMMEL work.
-As they descend to IBF, Takeshi swears once they save Coco, he'll go for Sora next. You and Takeshi talk, and they get into more techno talk about computers (the words "Neumann type quantum computer" pops up a lot.). Sora's apparently part of a 5th generation computer.
-You says Sora may have been developed in IBF, and LeMU was her testbed. In short, what You's saying is that they may find a way to save Sora in IBF. However, she says they need to take care of Coco first, and Takeshi agrees.
-Rest plays out the same up until they put Coco in the pod. Takeshi thinks he should look for a method to save Sora, but also remembers they're in a biohazard, so they can't stay too long. Everything else is the same until after Yoichi dies (though they don't find "T.Y"'s journal).
-After that, You and Takeshi talk in the hall. You says she's found a way to backup Sora, which Yoichi told her while the others were gone (the dialogue here is similar to the original). He says he remained in IBF to save his "daughter", Sora, as he was one of the staff members of Sora (You probably left the part out about him staying for her as well.)
-They go to the computer room, and You uses an ID card to access the computer. She says Yoichi told her there's a backup program in the room that can be used to save Sora. She tells him the researcher told her it was his way of atoning.
-She says the researcher told her he had a real daughter, but Leiblich invited him to join them shortly after she was born. They told him he was free to research whatever he wanted, which was too tempting to pass up, so he gave in and left his family to come to IBF.
-However, he said he regretted not being able to do anything for his real daughter or family, so he decided to atone by doing everything he could to save Sora, his other "daughter", though it might have been to preserve the one proof of his existence that resulted from his research.
(Way to be obvious, remake.)
-Just then, You finds the program, but says she'll need something to copy the data on. She says what they're copying isn't Sora, but the program, since Sora isn't on IBF's computers, but HIMMEL's.
-Takeshi finds a terabyte disc (which actually is in a case this time), and tells You, but she's silent. He sees she's looking at a photo on the desk, and the picture is a new CG: of a researcher (though his face is blurred out) holding what is clearly You when she was a baby. Takeshi doesn't make the connection.
(Hmm... so they're not really trying to hide that the researcher was You's dad this time? Is the game trying to use this to throw another twist our way? Is the twist supposed to be that the reason Yoichi stayed was because he was threatened by Leiblich? Well, this wasn't exactly one of the major twists anyhow... I thought it was You's dad in my first playthrough as well.)
-Once she snaps out of it, she says the disc will work. They copy the program and leave the room, and You says all he needs to do is put the disk into HIMMEL's computers. Takeshi wonders what will happen to Sora when he uses it. She says all of Sora will be copied into another computer.
-You says it'll be backed up into Sora's "sister", the LM-QSS17, though she doesn't know where the computer for it is. Takeshi wonders what will happen when the transfer occurs- You says probably either one of the two Soras will be erased, or they'll form separate personalities.