For reference it's around 10.20 into the episode, just after the half-way eye catch and the teleops stating 'the Instrumentality of Hearts and Souls begins'
Gendo: "No, it is not that we are returning to nothingness.
We are only restoring everything to its original state.
We are only returning to our mother, who has been lost to this world.
All souls will become one and find eternal peace. That is all there is to it."
Misato: "And that's the Instrumentality Project?"
Ritsuko:"That's Right. There is always a void, a part that has been lost to our hearts. [more teleops]
Every single person fears that darkness in their heart and lives life trying to escape from it, to banish it.
Even though it will never disappear as long as we remain human."
Misato; "That's why you're going to bundle all human souls together, so we can compensate for the void in each other?!
And you're just going to do thid to everyone?! Mind your own business!
That's nothing more than a conspiracy to deceive us!"
Ritsuko: "But you've been wishing for it to happen too."
In contrast to the rest of the psycho-analytical style of the rest of the episode, this seems to be playing out in the real world as in a scene where Misato confronts Gendo and Akagi about the Instrumentality project (this would be a natural conclusion to her story arc with Kaji and investigating Nerv, the Evas, Lilith etc) and I would argue it's probably 'actual' dialogue from the original ep 25 scenario included along with the real world images to give context. Gendo's line in bold also gives important info on the last minute reveal of Lilith. Also before the eye-catch, Shinji's lines describing the sensation of melting as Instrumentality commences might also be salvaged from the real world action of the original script.