@Eratas, the bullying part is just an excuse
he is just afraid of being too close with girls (Love Shy).
The reason why Alex end up in ISA: Alex can't escape. The governments are desperate enough to test all male within Ichika's age range to find a IS capable male. Once they found one, they threw him into ISA whether he like it or not (in Alex's case it is the former.)
Cipher enter ISA willingly after revealing prototype IS core (he wanted a harem, what is better to build a harem than entering an all-girl school?).
Imber take advantage of this to enter ISA to retrieve Pandora's Box (reason for him entering ISA has change: just my way of pitying him...
)
====