#all that to say : all hail Henderson as a positive educating figure

[midnight-in-town]

The Holy Trinity : project "Apple", "Eden" academy and "Garden"

In Genesis, the apple from the Garden of Eden is most commonly known as the fruit of knowledge and, to this day, we know Project Apple created experiments such as Anya (mind reader) and Bond (future seer). I'd say reading minds and seeing the future count as being "very knowledgeable".

Meanwhile Eden Academy is an elite school, represented by an apple on the students' uniform, in which parents of specific elite children (Imperial Scholars) have secret meetings (which Donovan has access to, thanks to Demetrius).

Also, as we know, Donovan studied there (and at some point gained telepathic powers too) and Henderson's flashback also taught us that there was a lot of war propaganda in the school back then :

Lastly, there is Garden, a secret organization, more of a legend even to a spy like Twilight, but who has super strong (no mental inhibitors ?) and probably indoctrinated soldiers, like Yor, working for them.

Eden Academy used to be pro-war and is today one of Ostania's most elite schools, super secret Project Apple wants world peace (probably meaning for Ostania to be in charge of that "peace")...

and Garden, a seemingly Ostanian organization, desires "to keep this world beautiful".

The link between all 3 can probably be summed up as "knowledge is power", which also sums up Twilight's entire mission as a spy for Westalis, trying to know what war Ostania (via Desmond who is confirmed to be able to read minds) is planning.

Lastly, the fact Anya's powers may be related to the use of classical language, a dead language most likely only taught in elite schools like Eden nowadays, is one more argument linking Eden academy (knowledge) and Project Apple (intellectual power).

As for Garden, they seem to specialize in physical prowess but if Yor's strength was indeed enhanced, surely it required a good amount of specific knowledge to unlock her mental inhibitors (and then to indoctrinate her).

(I'd also like to point out that Garden describing the world as a "beautiful place to protect" makes even more sense considering they probably took in several war orphans like Yor and made them "useful".)

TL;DR we don't know entirely how yet, but surely there is a link between Garden, Eden Academy and Project Apple and, according to Project Apple who wants "world peace", surely that can only mean war.