My current theory for if you choose to max out your Illithid powers is that you could end up turning into an Elder Brain. From what we see in the beginning of the game it looks like the Mindflayers on the ship are in a rush to reproduce and even have tech on board to speed up the process. Maybe they just needed more crew to man the ship or maybe the Githyanki attacks have pushed far enough into the Mindflayers' territory as to endanger the Elder Brain commanding them.
It would make sense then if the Guardian is actually the Elder Brain coaxing you along the path needed to become its successor. It wouldn't really be lying then for it to say it's protecting you as maybe in order for someone to skip along the Illithid lifecycle - from tadpole directly to Elder Brain - they first need to cultivate a great deal of psionic ability.
At the very least I think this would be pretty neat!
That's not how elder brains work at all. The way elder brains are created is more complicated. On average between 1 and 4% of successful ceremorphosis transformations become Ulitharids, they are essentially mind flayers that are about 1 foot taller, smarter, and have 6 tentacles vs the 4 of the usual mind flayer. Ulitharids then go on to live in a mind flayer colony in service to an elder brain. After a time one of the ulitharids can choose to take part of the colony away with him and set up a different colony elsewhere and at that point the Ulitharid extracts his own brain from his body and places it in a brine pool and from there the rest of the new colony takes care to feed the new elder brain so it can grow. But this is a rare occurrence. Most Ulitharids do not form new colonies or become elder brains.
Now in a highly unusual circumstance like this where a large amount of mind flayers came into existence without an elder brain to lead them, they would presumably be led by the Ulitharids among them and some of those Ulitharids would in time go on to become elder brains but that would take time it would not happen overnight and in the chaos the new Ulitharids would also not have necessary psionic black metal staves necessary for the process of extracting their brains, and the brine pools would need to be set up, etc.
