In the season final of "Angel", Connor is being deceived by his kidnapper-father Holtz and Justine into believing Angel murdered Holtz in cold blood. He is now even more vengeful against his true father - Holtz' plan worked flawlessly. He made sure as much as he only could Angel would never see true happiness, he took the dearest thing to him for the second time, even in death, and did it the most painful way possible.
His hatred only heating up, Connor is set on avenging Angel for the murder of Holtz and taking all his frustration, pain and anger on his true father. He's confused, Angel's personality, that so far has been contradicting everything Holtz has taught him about the vampire, left him thrown and not knowing which side to take, but the grief over losing Holtz, only feeding that confusion, forced him into an immediate choice.
He arrives at the Hyperion hotel, and accepts Angel's offer to give their relationship a chance. He moves into the hotel with his father and though he still maintains certain amount of distance from Angel, he's getting closer and closer to him, making the vampire to feel more and more confident in his son's loyalty. He deceives the unsuspecting Angel that a future is possible for them after all, and things do work out for the best sometimes.
Angel is going out of his way to please Connor as much as he can, finally being hit by a fear of not knowing how to be a father. He's trying his hardest, sometimes too hard even, to make Connor feel loved and welcomed, and it seems to be working. After all, they do become closer…only not for the right reasons. All Connor wants seems too be learning how to fight, more importantly - he wants Angel to teach him how *he* fights. Angel is excited he can share something like that with his son, teach him things, guide him, be a father, while Connor's true motive is learn his father's moves…so he can stand against him in a fight later.
Angel takes Connor to the drive in to see a movie, where Wolfram&Hart attack them. They're forced into a fight, where Connor is starring, protecting Angel almost for all he's worth, bringing him special pride when he tells Lynthon not to touch *his father* and that his name is *Connor*.
Things look only too good to be true, and they are. Angel's bubble of happiness blows in his face faster than he can follow.
When he goes to meet Cordelia, who never shows, in a place they set by the ocean, Connor arrives there and, out of the blue, attacks him. They start fighting, Angel is too confused to use his full strength and what's more, he's fighting his son, which makes it even more unacceptable. Eventually, Connor overpowers him, with the help of a stun gun, by electrifying him to unconsciousness. After Angel is knocked out cold, Connor signals to Justine with a flashlight, and they both board Angel's body on her boat.
When Angel wakes up, he finds himself in a box, chained up inside, while Connor is working on sealing him there. Angel tries talking to his son, but all Connor has to say is that he knows he killed Holtz and he will pay for it. Angel tells him he didn't kill Holtz, but Connor calls him a liar and doesn't want to hear it. With Justine's help, he finishes sealing the box, with his father inside, and tells him that death is too merciful for him, his punishment will be to live forever. Angel tells him that one day he'll find out the truth, and that he mustn't hate himself when he does, that he must remember he's his father and that he loves him. Connor, clearly is extremely upset and though he appears to be at peace with what he's about to do, inside he's not. Still, he pulls it off, and shoves Angel, in his coffin, to the bottom of the ocean, to live there forever.
His face is last shown as the boat sails off into the night, and he impassively gazes at the spot where he threw his father into the water.
Angel: Some day you'll learn the truth...and you'll hate yourself.
Don't. It's not your fault. I don't blame you.
Angel: Listen to me. I love you! Never forget that. Connor?! Connor, never forget that I'm your father and that I love you. Connor? Con...