(More DVD extra-ish stuff on Taking Sights)
One of the operating assumptions of Taking Sights is that, in canon, Gendo and Yui started out with good intentions, that they planned to screw over SEELE and stop Third Impact. But... there's no proof of that in canon.
Consider our three sources of information on the activities of Second Impact (SI) era Gendo and Yui.
1. In "Death & Rebirth" we overhear (to a video of the fabled Contact Experiment at the Katsuragi Expedition base camp) Gendo and Keel waxing philosophical about the arrogance of science. While this bit gives us insight into Keel, it's questionable what it tells us about Gendo. He could be playing along, he could agree, or he could agree with what Keel's saying but still think he's wrong wrong wrong about Instrumentality.
2. During Fuyutsuki's interrogation, we learn about Yui, Gendo, and Naoko running the Artificial Evolution Lab in what will soon become Tokyo-3 and the Geo-Front. Gendo talks about "Mankind's New Genesis" to Fuyutsuki. This information, too, is suspect. Why? Because Fuyutsuki isn't a reliable narrator. Remember, he's supposedly relating all this to SEELE (who are demanding to know if Gendo has a secret agenda). It's not like he's going to tell them (and, by association, us) that Gendo & company are planning to mess up their masterplan!
3. The Yui/Fuyutsuki flashback conversation shown in the epilogue of EoE. This scene can be read as going either way as far as Yui's ultimate intent regarding Instrumentality (or some form of it). She and Fuyutsuki are mainly talking about her ending up inside Unit-01 for all eternity as a symbol of mankind's existence. Otherwise we don't learn much about her or Gendo's plan.
So, really, Gendo and Yui Ikari cannot be seen from canon evidence as either fighting for
some form of Third Impact. We know Gendo is opposed to SEELE in 2016 with his "Death Creates Nothing" line, but he says that while he himself is planning his own Third Impact which, aside from his intention on getting back with Yui, we don't know what he was ultimately planning to do with. Or even if
he had any other plan aside from "be with Yui".
So why, in Taking Sights, did I take the tact that Gendo and Yui were opposed to any sort of Third Impact? Well... because otherwise there wouldn't be much of a story.
If Gendo decided upon Peggy Sueing himself that he needed to work towards a constructive Third Impact then he'd still be something of a villain. And while it'd be interesting from a storytellers viewpoint to write about a villain like that there'd be two problems. First, Gendo wouldn't be changing nearly as much (changing himself and the world around him). Second, there'd be an assumption (and expectation, really) on the part of the audience that at some point in the fanfic Gendo would doubt, question, and then change his mind about Third Impact as his relationship with Shinji evolves (which sounds boring and predictable to me, but I'll admit I can see some potential in the idea).
There's also another big reason I made Gendo anti-TI. Taking Sights is a Peggy Sue
story. More specifically, it's my attempt at a subversion
of the conventions of the Peggy Sue trope (as well as several other standard NGE fanfic tropes
At its heart, a Peggy Sue requires that the time traveler try to change the future for the better
. If Gendo has to be convinced that Third Impact isn't really a good idea, then we'd have spent 75% of the fanfic getting to the starting point of the Peggy Sue trope -- the hero deciding to make the future better, no matter the cost to themselves. And if I'd, say, made it that Gendo (and Yui by extension) think causing a constructive Third Impact IS
a better future then he'd have no real reason to interact with Shinji and muck around with the timeline. Taking Sights would be a lot
shorter then. Instead, to do all the subverting and deconstructing
I wanted to do about Peggy Sues (a common fanfic trope) I had to make Gendo "hero-ish" from Day 1. That way I could have him try to be a better person and then (instead of like the Peggy Sue protagonists in "Once More with Feeling
" or "The Second Try
") have him totally fuck things up
Plus, what sounds more interesting in your "hero":
1. Him and his dead wife being a different sort of fanatic than the other villains (SEELE) but still dedicated to what amounts to the death of the human race.
2. Him and his dead wife plotting for 17 years to stop & kill fanatics that want to destroy the human race. Only... in order to save the human race... they have to play along with the crazy fanatics for years, even actively help those fanatics kill half the human race
... just so that, in the end, they can save the survivors from a Fate Worse Than Death at the hands of the fanatics?
This may just be me, but #2 sounds much more interesting as a character motivation for Gendo Ikari (at least before the whole dead wife business kicked in).
So now you know why I made Gendo (and Yui Ikari) originally intend to stop the Third Impact.