LOL it’s no problem dude I’ve watched the series multiple times and any concrete understanding of the Human Instrumentality Project still eludes me. But it breaks down as follows:

• The Human Instrumentality Project is SEELE’s plan to bring Third Impact under its control and usher in a new stage of human evolution: the consolidation of all souls into a single, immortal, incorporeal, and godlike being.

• Third Impact is effected by the union of an Adam-derived being (i.e., one of the Angels) with Lilith. Lilith’s Black Moon, the “Fruit of Knowledge,” is not meant to exist on the same planet as Adam’s White Moon, the “Fruit of Life.” I guess the First Ancestral Race fucked up when they tried to seed earth with one of their Moon spaceships, because the black one crashed and embedded itself beneath Tokyo-3. Since you can’t have both life- and knowledge-based life forms occupying the same planet, the FAR added two Spears with the Moons. These Spears are meant to inactivate one of the seeds in the event of a screw up. However, Lilith’s Spear was destroyed in the Black Moon’s crash landing, and so Adam is impaled in suspended animation while Lilith’s progeny — humans — populate the earth. (Hence the term “Lilin” that Kaworu uses for humans.)

• Adam’s children, the Angels, seem very pissed off about this whole screw-up and are thus clawing desperately to get at the crucified Lilith deep inside NERV headquarters. Earth was meant for THEM, damn it!

• Think of Third Impact as a massive hard drive wipe and reboot sequence for planet earth, and the Dead Sea Scrolls as the extraterrestrial instruction manual and programming code required to initiate that sequence (and to make use of the Spears and Moons in general). Basically, SEELE wants to implement and also rewrite some of the code to suit their own wackjob agenda. They all probably took too many drugs and listened to too much Terence McKenna, because they seem to think dissolving into a puddle of unified primordial ooze is an ideal scenario.

• Gendo Ikari doesn’t give a fraction of a shit about what SEELE wants — or what anybody else wants, for that matter — and is looking to rewrite even MORE of that program code in order to reunite with Yui inside Unit 01 (which contains her soul after the freaky deaky contact experiment). In order to do this, he intends to use the Adam embryo — fused into his hand — and Rei, who is a clone of Yui with the soul of Lilith. 

In essence, all the assholes of the series want to use the reboot sequence for their own ends, while our heroes are conveniently kept in the dark and convinced they are doing their job to defend the earth from HUGE AND ANGRY AND OCCASIONALLY GEOMETRIC SPACE ALIENS.

I prefer not to mire myself in the convoluted mechanics of Human Instrumentality, and instead conceive of it in a more abstract manner. The Project is a symbol for the misguided attempts at the elimination of anxiety and fear — fear of abandonment, loss, death, and oblivion — that is caused by individual consciousness; of being a comprehending (and thus, godlike) soul trapped in a rotting, ephemeral case (the human body). The antagonistic parties within the series just have slightly different and destructive ways of eliminating that fear because they are all huge babies.