Family
Jedi have no family. Taken from their parents in infancy, they are brought up communally, and attachments of any kind are very much frowned upon.
Officially.
Should one dare to listen closely enough, however, the Living Force sings a completely different story. From Masters to crechelings, all Jedi form their own support network, as any sentient is wont to do, and where ties of blood are absent those of the soul flourish, never recognized but nonetheless cherished. Initiates and Padawans, Knights and Masters, all are linked through a complex web of hierarchy and friendships, and most, if ever forced to consider such things by some strange twist of fate, might be able to name, if only privately, a parent, a sibling, a child.
They will never admit it, however, not even to themselves, for family is not the way of the Jedi as the modern Code prescribes it.
XXX
Right from the beginning of their training and up to their deployment on the battlefield and beyond, clones are encouraged – conditioned, really – to consider their fellow soldiers as Brothers. To them, it is only normal to see their comrades as family, and no clone would ever consider rethinking that point of view.
To them, their attachment to each other is a way to keep going when all else fades in the absurdity of war.
Best mates will stand together no matter what. Squad members are inseparable. Batchers will often keep in contact, even when assigned to different parts of the galaxy, and an officer will always, always watch over his subordinates, and they over him.
XXX
When the Jedi are tasked with leading the clone armies, no one sees anything coming – of course, between the former's policy on attachments and the latter's respect of hierarchy, there is very little an outsider could see.
It does not happen instantly; it takes weeks, months, years to develop, following the terrible rhythms of battle and the interminable waiting in-between. It happens very gradually, so that very few are those who see.
It does not happen everywhere either, of course: those discussed here are, despite appearances, individuals, and sometimes wildly different ones.
But it does happen.
Somewhere in the midst of chaos and destruction, on the long campaigns that erode strength and break down lives, the carefully erected barriers fall. Friendships flourish, and bonds that go deeper than they should are formed.
A clone might talk about his unit as his Brothers, and forget to exclude his Jedi superior officers from the lot.
A Padawan might eventually go from "Sir" to "Kid", and become seen as a cadet – a younger sibling – to help train and protect.
A clone commander or captain may become their Jedi's mission partner, even when the rest of their troops has no reason to get involved in whatever trouble the General has managed to dig up this time – some would say that is merely the logical course of action, in a time where overburdened agendas make it difficult for two Jedi to work in tandem as they would once have. Those involved don't know better only because they refuse to acknowledge it.
A Jedi General trusts their clones with their life and sometimes that of their Padawan, not to mention the fate of the Republic, and their men would follow them into the craziest of plans in return.
… Under the radar, without anyone (including themselves) being the wiser, the clones adopt their Jedi officers and vice versa.
For three long years, they face War together.
XXX
The Jedi Order is not the only thing destroyed by the biochip.
When it activates, it essentially short-circuits the clones' personalities and capability to feel emotions, leaving them as little more than organic droids, programmed to follow orders.
Most Jedi die without ever noticing anything, preoccupied with their environment and trusting their men to have their back.
Many Jedi die feeling betrayed, reeling from the shock of their friends' sudden attack.
Some Jedi get the time to realize that their brothers-in-arms are suddenly gone, replaced by empty Shells. They die confused and horrified.
Very few Jedi survive Order 66. Those shall remain scarred for life.
XXX
The human brain, however, is adaptable; within months for some, years for the others, the biochips start failing.
Clones start waking up.
Most clones do not remember, and certainly prefer it that way – the nightmares are bad enough as they are.
Many clones are suffocated by guilt, knowing without remembering that they betrayed and killed people they saw as not only superior officers, but also as siblings, and did so in the most horrid manner possible.
Some clones will not let the horror get to them and start looking for answers, figuring out what happened and helping the few survivors they find, or even sometimes just plain untrained Force-sensitives, to disappear, out of the Empire's reach.
Very few clones cannot find it in themselves to heal and keep going, in the end. Those their Brothers try to bury with dignity, when they can.