The school dates back to at least the 1940s or 1950s, when Cornelius Tower founded it as a haven for people with extraordinary abilities, with the apparent goal of bettering humanity. However, the school was later taken over by "corporate lackeys" whom Cornelius Tower saw as corrupting his ideals. ("Dreams")
The Tower Prep is run by the board of directors and the current Headmaster, with the primary goal of training and enhancing the special abilities of its students.
Further, Headmaster is secretly working with Cornelius Tower, so his real goals are different from the board's, although they don't know it yet. ("Fathers")
There is no graduation ceremony. Each year, the graduating seniors simply disappear. ("Book Report")
Show creator Paul Dini elaborated on this in a podcast in 2013. Cornelius founded the school to be a place where children with special gifts would be trained. Upon graduation, they would be sent out into the world -- in secret -- to help guide mankind toward a better future.
Possible locations that match those latitudes and also border an ocean or sea include: British Columbia (where the show is actually filmed), Newfoundland and Labrador, Southern Ireland or the United Kingdom, Northern France, Belgium, the Netherlands, the Eastern coast of Russia bordering the Strait of Tartary, Sakhalin, and the Kamchatka Peninsula.
Do the students' parents actually know about Tower Prep?
Suki's parents know about her whereabouts because their company SatoSystems is involved in running the school, and her brother Shinji also knew she was there.("Phone Home")
Headmaster claims that all parents know where their children are, however if that is a true statement is yet undetermined. ("New Kid")
When Ian called his mother, she told him that the call he made was dangerous, before saying "Merry Christmas", confirming that it was really her, and hanging up. Therefore, his parents definitely know something is going on, though it's not clear how much they know, whom they believe is in danger, or if they actually know where he is.("Phone Home")
Headmaster keeps a phone in his office, and when a student demands to talk to his parents, he lets them use it. However, all it does is connect them to Whisper who mimics their parents voice in order to trick them into thinking it's their parents, who want them to be there. However, Whisper did not know about Ian's mom's tradition of saying "Merry Christmas" on his birthday, tipping Ian off that is was a trick. This may imply that either the parents don't actually know where they are, merely that they are gone, or that they know but it was not their choice to send them to Tower Prep.("Phone Home")
The Broken vanished from their temporary base in the old gnome bunker.
A gnome was encountered patrolling nearby, hinting either they were captured, or had been forced to vacate to a new base.
Headmaster told the board of directors that the Broken had been "mended," and that Ian was also "broken" and would be taken care of. However, there is the possibility that he could have been lying in order to give himself more time. ("Trust")
Emily Wright joined the Broken, and also disappeared when they disappeared.
CJ asks Cal if the Broken were hurt, implying she also told him about the hidden bunker.("Snitch")
Rooks are a secret fraternity said to have existed since the school began.
They use Corvus H-40, (mixed in with Raven's Blood) to enhance there abilities. They most likely obtained this from in the tunnels beneath the school. Down in the tunnels, Ian finds records that it was used on students, including Coach. When Ian asks Coach about it, he states that it is a performance enhancer and that it is banned from student use. However it is revealed that Coach either lied or didn't tell the complete truth to Ian. ("Rooks")
Their symbol is the raven. Because the raven image contains the initials CT, it may have originally been Cornelius Tower's personal crest. However, it's unknown whether the current Rooks understand its meaning.
Jeremy was the current leader (referred to as Odin or Most Exalted One) until he attempted to crash CJ's dance but was thwarted by Gabe's hypersuasion. It is unknown if the Rooks have appointed a new leader. ("Rooks")
The leader of the Rooks is refered to as Odin, who was the one-eyed king of the Norse gods. Cornelius Tower also had one eye, which may symbolize a connection between the two.
Their appears to be a senior version of the Rooks amongst the faculty. ("Rooks")
Headmaster is leader of the senior Rooks. Coach is also a member. It is unclear if the older Rooks simply had been members of the fraternity back when they were students, or if they are still in contact with the student Rooks.("Rooks")
Cornelius Tower claimed to have created hoaxes like the cyclops skull to fool the world into thinking he was just a crackpot eccentric. ("Dreams") It's likely that the graveyard is full of his faked zoological creations, which would explain the fake species names on the grave markers.
The grave markers have Latin names engraved on them. The names Ardipithecus hominis and Robustus rosensus are similar to scientific names used to classify living organisms, but do not match known species. "Ardipithecus" is a genus of hominins, early ancestors of humans and chimpanzees that lived approximately 4 million years ago.
CJ claims that she does not remember anything from her life before Tower Prep. However, this is a ruse, and CJ is actually Headmaster's daughter, who is sent to spy on other students who are planning to escape the school. ("Snitch")("Fathers")
Clues planted earlier in the series include the following:
When convincing Headmaster to let her arrange a school dance, CJ tells him "I'm owed this." ("Rooks") She later repeats that she's "owed" a normal life because she's had to give up so much to be Headmaster's spy. ("Fathers")
Unlike her friends, CJ has no dreams about escape and the yellow elevator. ("Dreams")
CJ stated that she knows her dad "would not understand if she left Tower Prep." ("Trust")
Gnomes act as guardians who stop students from entering forbidden areas and protect the school from outside threats such as the Broken and the Exiles. ("Field Trip")("Snitch")
Gnomes take orders from Headmaster. This is proven when gnomes capture Conner Owens, and Headmaster is then heard ordering Dr. Specs to interrogate Conner at West Campus without Mr. Sato finding out. Therefore the gnomes almost certainly take orders from Headmaster or someone working for him. ("Snitch")
Gnomes are Tower Prep students, as proven by the radio chatter heard through the Gnome translator. ("Buffer")("Field Trip") The only unanswered question is exactly which students become gnomes and under what circumstances it occurs.
Ian unmasked a gnome, revealing that it was a student, but not one whom anybody had seen before. ("Trust")
Cal Rice became a gnome voluntarily. Cal eventually returned as a student, claiming not to remember anything about becoming a gnome. ("Trust")