During a battle with an Angel, Rei's entry plug is ripped from her is sent flying and lands in a lake.
"Urgh...my head..." Rei complains once she is reoriented.
Rei sees that there is a hole in the entry plug, leaking in water slowly but surely.
"I've got to get out of here before the plug fills completely!"
Rei is about to go unlock the plug entrance manually, but finds she cannot.
Rei looks down and sees that her right foot is stuck in between two dents in the entry plug.
"Rrgh...I-I'm stuck!" Rei exclaims while struggling with her trapped foot. She pulls and pulls, but while her foot does not hurt, it is stuck quite securely.
"This isn't good," Rei thinks. "If the plug keeps filling up at this rate, I'll be drowned within two hours." In desperation, Rei looks around for anything to help her.
The plug's contact systems were shorted by the crash, making it impossible to communicate with Misato or NERV in general.
There is nothing in reach for Rei to pry her foot free with.
In a few minutes, the water level in the entry plug rises to Rei's ankles.
Rei continues struggling with a valiant effort, but to no avail.
At this point, Rei begins to panic. What if NERV doesn't start looking for her? What if they find her, but not in time? What if...this is the last day of her life?
Rei remains in this panicked state for a while, before coming to reality.
Of course NERV has to look for her. She's one of the only three pilots of the Evangelion. If they lose her, the UN will be on them and then they'll be in trouble.
Reassured, Rei continues working on freeing her trapped foot.
About an hour passes, with no success.
The water level is now up to Rei's waist. She begins to start panicking again.
"Why hasn't NERV found me yet?" Rei wonders
"With all their high-tech equipment, I think they'd be able to track me down by now."
With her lower body now completely underwater, struggling against her stuck foot is near impossible. Rei decides to stop fighting it and give in.
Another half hour passes. The water level is now just below Rei's solar plexus. Her plug suit is drenched and worn down from exposure to the grainy, impure salt water. Rei accepts that this will be her death. She starts reflecting on her life.
"I wouldn't call it a good life." Rei thinks. "It was full of sorrow and misery. Always in pain, always alone. Always the outcast."
"Until I was recruited by NERV."
Rei starts thinking of her companions at NERV.
"Asuka Langley Soryu. Obnoxious. Loud. Eccentric. I never really liked her..."
"Gendo Ikari. Possibly the closest thing to a friend I've had. I enjoyed our conversations before missions."
"Misato Katsuragi. I know she forced Shinji and Asuka to live together. A very whimsical person. Not really a friend of mine."
"Dr. Ritsuko Akagi. A strong headed woman. She appears to know where she is going. Somehow, she is friends with Miss Katsuragi, though they appear opposites."
"And finally..." Rei says.
"Shinji Ikari."
Rei pauses for a moment.
"I never really knew him. All I know was that he and Asuka couldn't stand each other. Still, there was a certain...feeling...I had about him."
With her memoirs completed, the water level rises to Rei's neck.
"I suppose this is it..."
Just then, a NERV team breaks open the lock to the plug, then reseals it.
"Ayanami Rei? We're here to save you."
Shocked but relieved, Rei replies. NERV has not forgotten about her.
"Thanks, but that'll be harder than you think. My right foot is stuck tight."
"Don't worry. We're prepared." the NERV team responds.
They send a member down into the plug, with a prying tool. Within seconds, they free Rei's trapped foot and get her out of the entry plug.
After her rescue, Rei is brought to the infirmary, where she stays for about two days until her strength is back up.
In reality, Shinji and Asuka were defeated by the Angel, and NERV was trying to find a way to defeat it. This is why they took so long to find Rei; they were forced to prioritize the mission over one of their pilots. Luckily, due to one of Misato's convoluted plans, they were able to defeat the Angel within two hours and save Rei.
Rei's plug suit was full of tears and and holes due to exposure, and she was issued a new one.
Shinji admits that he argued to try and save Rei before destroying the Angel, but his proposal was shot down by Akagi and her prioritization.
Asuka brags that she would have found a way out and that she would be more careful where she stepped, although inside she is glad that Rei was fine.
Shinji is elated that Rei is alive and well. He wouldn't have wanted to be left with only Asuka as another pilot. Still, despite this, he feels another slightly...different...feeling toward Rei being safe. He decides to dismiss it and carries on.
Within a few days, things are back to normal at NERV. However, Rei will never forget the near death experience she endured on that day.