Our whole species is known as Lilins. Our name comes from our Great Mother - Lilith. Originally we were all one, giant mass, that lived happy live, without any worries, lacks and imperfections. We were all a perfect organism, which arrived on Earth. However due to Lilith's arrival on this planet, billion years ago, her own blood (known also as a LCL) was spread around the globe. It eventually evolved into the first single-celled life on Earth and ultimately into a human kind. This event is known as a 1st Impact.
As you can clearly see, we all come from one existence, we are all one and one organism only, which is scattered on Earth. This knowlage may help you better understand what Human Instrumentality Project is about. Our main goal, as an ogranisation is to initiate a situation, where we can cause great, 2nd Impact. As the 1st Imact caused separation, we want the 2nd one to cause fusion of all people. Long story short it is all about coming back to our pristine form. Form of a one, perfect organism.
Probably this is the question that interests you. The answear is really simple. As humans, "individual" creatures, we all feel pain, emptiness and we strive for being loved to avoid bad emotions. It is impossible to do, no matter how hard we try. Suffering is included in our existence. The only way to get rid of it is by becoming integrating into one creature. Even if you find someone you love and you are also loved back, this feeling is not as strong, as in your primary form - Lilith. It is not immortal emotion, not even a long lasted one. Thats why our species feels pain all the time. We alone, can't fill this emptiness in our hearts. The only way to do it is to reunite, to come back to LCL form.
As for the plan itself I can not say much due to regulations of NERV's privacy I can however reassure you it is going to be a painless action with most benefits for everyone. Like I mentioned before, this concept, that we are working on was found by people who wanted to make an earth a safer place and give our lifes better meaning.
When it comes to realisation itself, you can read about it more in my researches which I am currently working on and updating.