A Shakespearean actor takes poetic revenge on the critics who denied him recognition. Theare of Blood
Nibelheim is home to many Shinra tragedies. It's been rebuilt and restored and might be the poster boy for cover ups. I'm starting to think that Nibelheim is cursed. Vincent and Cloud also make this statement sharing the belief that nightmares and sins are born there. It is through Vincent that we learn Sephiroth's mother is not Jenova but Lucrecia. Thirty years before Cloud went back to Nibelheim a second time (according to Vincent) Vincent was detailed to protect the scientists working on the Jenova experiment. They were stationed in the outskirts of Nibelheim in the old Mansion. After a love affair and being unable to save the woman he loved, Vincent felt he needed to atone for his sins. The birth of Sephiroth is a large point in this story, as it shows specifically who his parents are (well his mother for sure). Vincent tells Cloud and party what happened. That is to say that Lucrecia gave birth to Sephiroth for sake of the Jenova project and he was unable to protect her. He then hears Cloud's account of Nibelheim burning at Sephiroth's hands in which Vincent adds more sins to his list. Vincent's involvement in Nibelheim serve only to shed light on Sephiroth's birth and give him hatred for Hojo.
Vincent fell in love with Lucrecia and the two would spend time together. In the original game, Lucrecia has no real reason for leaving Vincent for Hojo, stating nothing more than that they're both scientists and that Vincent wouldn't understand. She becomes (or is) pregnant with Sephiroth, who will be the breakthrough for their work. Vincent, angered and concerned for Lucrecia and her child, confronts Hojo. He tries to reason with Hojo that experimentation on people (perhaps more likely Lucrecia) was wrong. Hojo shoots and experiments on him. In Dirge of Cerberus it is revealed that Lucrecia leaves Vincent because of her involvement in his father's death - the guilt pushes her away. Yet after Hojo experiments on Vincent, she tries to save him by giving him the Chaos gene, this allows him to transform into his ultimate limit. Vincent goes to sleep (or is put to sleep) and put into the coffin in the basement. Sephiroth is born to Lucrecia and taken from her. But the only things he knows for certain are that Sephiroth is Lucrecia's child and that if he goes with Cloud he can make Hojo pay. He doesn't know whether or not Lucrecia lived or if he'll be able to do anything, but he goes with Cloud because he thinks he'll be able to meet Hojo again.
I have always believed that Hojo knocked Vincent out again and put him in the basement, as the clues on the scraps of paper in the first left room seem to be more akin to a game. Rather that it's something planned. Unless, Hojo put him to sleep and locked the door, which is likely. It seems unreasonable to me that Vincent would willingly stay there if he were awake. I suppose because he thought she was dead he had no reason for moving from his spot and sought to live out his days locked away. Still once he meets Cloud, Vincent resolves to get revenge on Hojo.
I also think it likely that Hojo knew about Vincent and Lucrecia's relationship. News travels fast in small towns. In particular, I don't believe that Hojo cared one way or another about it. Nor do I think that he cared what happened to Lucrecia as long as the child lived. Unchallenged, I doubt Hojo would have done anything. When Vincent stood up for Lucrecia, though, I think Hojo decided he had to do something otherwise Vincent would have. I could see Vincent taking Lucrecia and her child away. If he meant to save her, it would be possible and I think that would have been his next step had Hojo not knocked him out and ran experiments. I think that Hojo knew Vincent would continue to intervene and champion for Lucrecia. This is also why I believe that he made a game of locking Vincent away and then leaving clues on how to find him.