toot m

They were a pre-war research firm. Bright minds that went into an underground facility when the bombs fell. Over time they expanded downward. They continued to research cybernetics, robotics, agriculture, cloning, weapons, power sources, teleportation, and many other fields of research, since that's what they were good at. They just continued being a thinktank after the war.

Over time, they decided to research making advanced robots not like the pre-war robots and so they made gen1 synths. These served well for a time, and they even made a second generation of synths with more fluid movements and physical capabilities, until their power and mechanical repair components became an issue. Eventually, the institute faced a power and mechanical repair resource shortage, despite the best efforts of the brightest minds.

Around this time, they sent their fancy new gen2.5 synths to work with the surface to rebuild. These scientists wanted to put their big brains to work rebuilding the world, but they didn't want to expose themselves to radiation by actually going up there, so their vaguely human looking mechanical robot messengers proved perfect for this. Eventually one malfunctions and accidentally kills a bunch of people, and around this time one also is the mysterious sole survivor of a shootout at the CPG meeting, so the toot is the prime suspect. Records indicate neither of these events were intentional, but the toot leadership is too autistic to navigate this situation, so they hide underground when people are mad at them. Over time, they become afraid of these mad people with their torches and pitchforks, so they devise a plan to get some heat off of themselves.

Shortly after this time, their gen3 synth program was advancing. They had conducted lots of research on FEV and were making strides in creating fully organic labor force to replace robots. Rather than euthanize their super mutant FEV test subjects, they instead divert much-needed power to the mutant's life support systems until they are mature enough to fight, and send them to the surface to distract surfacers by killing them. Around this time the gen3 synth program (the result of the FEV research that involved super mutants) was up and running, so they adapted a few individuals from their new organic labor force to be surface infiltrators, where they could sow seeds of misdirection to distract the surfacers and convince them the institute is just a rumor. This capability also proved useful in research, where they murdered a few individuals like Roger Warwick for research purposes as well.

As of the events of Fallout 4, the motivation of the institute are:
1. Become self sufficient. Find a new power source to fuel their underground facility.
2. Related to that, replace the robotic labor force with an organic one, so they can reduce power and mechanical components
3. Keep the surface distracted with super mutants and infiltrator synths
4. Continue their research. They are scientists who want to learn and make new inventions
5. Live underground for as long as they deem necessary, ensuring their underground facility is equipped to do so. They believe the surface is dead and the people up there are dying, but the long term plan far in the future may include retaking the surface if they so desire, and the gen3 synths are perfect for that because they have a natural resilience against radiation

On a personal level, specifically Father's motivation is to find a new leader for the toot. He is dying, and wants someone who can take the toot in a bold direction to take over for him. He knows his staff well, and knows how each of them would handle being Director, and for whatever reasons, he is unsatisfied with each of them. They are insular, they are petty, none of them are charismatic, most of them have poor social skills, and various other things like this. He wants someone new, fresh blood, to lead the toot. Someone with a unique skillset. Most wastelanders are illiterate morons, so he chooses none other than his own parent, stored nice and frozen with their pre-war education and pre-war lack of mutations. And who better than his own family? The hubris shows a bit here but he's technically not wrong. Nate/Nora are likely a lot more intelligent than your average wastelander, and they also have pre-0war socialization which will be a bonus for being the leader of an organization for a plethora of reasons.