If you have completed disk two you will know that Hojo is Sephiorth's father.He had always neglected Sephiorth though and was a bad father,he didn't even tell Sephiroth the truth about any of his parents.Perhaps he wasn't such a bad guy though,and there's a bit of proof.
Hojo married Lucrecia almost as soon as he met her,she must have had the hots for him because she was already going out with Vincent.She dumped Vince though when she met Hojo.After that,before the injecting Jenova cells thing started,Hojo got Lucrecia pregnant.Lucrecia always loved Sephiroth more than anything,she had probably always wanted a child so maybe Hojo decided to bring her a little happiness.
Hojo then offered Lucrecia to Professor Gast's Jenova project and the unborn Sephiroth was injected with Jenova cells.Hojo ignored Sephiorth's needs but if you have killed Hojo you'll remember that he died trying to help Sephiorth achive his goals.This has gotta be some sign of good fathership,right?
Also,does anyone remember that Hojo cloned Sephiorth after he was reported dead?Hojo wanted to make a reunion for Sephiroth,as well as being part of an experiment,maybe Hojo thought that the clones would make Sephiroth stronger.
You don't see Hojo often in the game but when you do see him,there are a few times where he's helping Sephiorth and before he dies,shortly after he injects himself with Jenova cells,he tries to help Sephiorth and he calls him his son.Who knows,maybe Hojo had a bad family history himself? Hojo always put himself down as a failure when it came to science so maybe he wanted to prove himself so much that his work overpowered him...
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