I think he’s sad over his past, rather than his father. The world he knew for many years, almost his whole life to this point, was the human world. Suddenly, though, the human world has passed him by by 30 years which to him felt like 3. In what felt like 3 years he was entirely left behind by the entire human race. It’s unimaginable what all he has missed while it felt like he’d just taken a nap. Life, death, grand and horrible human accomplishments, the advancement of technology...the place that was once his own would now be pretty unrecognizable. It hurts to feel left behind or abandoned or cast off. I think there’s definitely a parallel there to his relationship with his father here, but ultimately I think it’s much more than just his father.

Wait does this means Mako's father what the one that kill him in real life?? Im a bit confused