While she doesn't ally herself with Karl, why does Altera stay by his side? Because she knows that it's Lonely at the Top and, in her own way, she wants to remind him that You Are Not Alone.
Altera's strong, familial relationship with both Charlie and Karl as a whole.
Lu Bu's Servant conversations wherein he expresses both praise and gratitude towards Hakuno for being such a great tactician.
Darius III barely ever says a word in his Servant conversations, but Hakuno repeatedly comments about the touches of humanity that remain in his eyes behind the Mad Enhancement.
Reaching a Max Bond with Karl shows one of the conversation that the emperor no longer wants to treat Hakuno as his Master, but rather wants to adopt him/her as his son/daughter.
Surprisingly, Archimedes first shows off a bit distant and logical during the Bond Conversations, but as the Bonds increase, he slowly shows signs that he's willing to help out and accompany Hakuno to battle in his own way, and is even conflicted with himself if he wants to return to solitude or continue aiding the Master.
In a weird way, Bathory throughout the game. In the first Extella, when Li Shuwen treated her with respect and gave actual, serious criticism instead of just telling her how much she sucked, she actually responded positively to him and treated him in respect in return. Turns out this was the key to her whole character. Because when Hakuno is forced to take Bathory into his army, they do so with much snark but little by way of actual insult or disrespect. The end result is that Liz entirely avoids her Chronic Backstabbing Disorder and remains a steadfast, capable, and loyal officer throughout the whole game.
