In the Anime, after Evangelion Unit 01 eats Zuruel's S2 Engine in it's beserk mode, Gendo is seen in a meeting with the member of SEELE or whoever the pseudo-illuminati style organization is running NERV from the shadows. One of the directors of the organization states Evangelion Unit 01 has become self aware, almost becoming god-like, and that they have no use for a god in their master plan.

Now I fail to see how a sentient EVA Unit can prove to be such a hindering factor in SEELE's ultimate plan. How could one EVA Unit pose such a threat to the plan that the Unit had to be grounded until further notice? and what type of hindrance were the SEELE directors talking about?

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    if i recall grounding Unit 01 was less about it being a hindrance and more about preserving it. not only did Unit 01 develop it's own S2 Engine but also Unit 02 was out of action (for a while) after being decapitated by Zuruel and given the importance they were putting on Unit 01 i would suspect they didn't want to expose it to potential risks as being destroyed by an angel – Memor-X Oct 19 '18 at 10:00

So, after reading the manga extensively and going into detail about the meta of the episodes close to the end of anime, I think I finally pieced together the reason why EVA Unit 01 was grounded by SEELE, and how EVA Unit 01 interfered with SEELE's plan.

In the manga, EVA Unit 01 was grounded by SEELE as a form of "insurance" for executing their version of Third Impact, only to be used in case Gendo Ikari executed his version of Third Impact. EVA Unit 01 was grounded based on the fear that Lillith might become compromised should Gendo go ahead with his version of Third Impact.

This also explains why EVA Unit 01 is the only Evangelion Unit to made from Lillith as opposed to being made from cloning Adam.

I think that EVA Unit 01's awakening phase was not accounted for correctly by SEELE in their master plan, and therefore was grounded to readjust and incorporate an awakened Unit 01 into executing Third Impact. I also think that SEELE was afraid that both EVA Unit 01 and Lillith may be compromised, and thus tried to control what they could from the shadows as best they could, whilst still ensuring Third Impact (i.e. grounding EVA Unit 01)

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