I know there have been plenty of topics on this already, but the most recent one is closed and I want to share my own theory. First off, some of what I have here I pieced together from his final words, which I am reposting from Darnell Putman in the previous Clockwerk theories forum: "I am... been selling... Flowers... Never... reality... I will become... Feet together... I will live... Redirect Energy." The three phrases from this that are most important are: "been selling", "flowers", and "feet together."

For my theory to work, Sly has to be back in the present, however long it takes for Bentley and the rest of them to find him and bring him back. Once he's back in the present, the gang meets an owl couple. For the sake of discussion, their names will be Fred and Julia. (Yes, "Fred" will eventually become Clockwerk, but I don't think he was born with that name. I think he gave it to himself eventually to make himself sound more threatening.)

Eventually, they become a part of the gang, although Sly, Bentley, and Murray are obviously hesitant to let them in. However, since Clockwerk is dead, they don't see the point in keeping owls apart from their group, and the couple seem more than happy to help. Julia becomes a part of the field team, while Fred is more of a techie, so he sticks with technology, often building gadgets and selling goodies on ThiefNet that the gang manages to collect.

Soon, he decides to ask Julia on a date since they hadn't been out together alone since joining the gang and gets Bentley to take over his jobs while he goes to buy her flowers. However, while he's gone, an enemy attacks the Cooper Gang's hideout, and while they manage to repel the enemy, Julia ends up dying in the attack. Fred is depressed when he finds out and, while he doesn't leave the gang, he does isolate himself, silently fuming, blaming himself for not being there to protect her.

Not too long after that, Fred slowly starts to reflect the blame from himself to Sly, thinking that since he's the leader and was present during the attack, he should've been protecting Julia. Soon, Fred flies away from the gang without a word. He builds his own fortress and eventually kidnaps Carmelita, who at this point is probably Sly's girlfriend/wife, wanting him to know how it feels to lose someone he loves. When Sly tries to rescue her, Fred, just like in Sly 1, fills the room with poison gas in an attempt to kill Carmelita. Bentley stops this, of course, but the kidnapping and the poison gas solidifies Sly's fears that Fred is Clockwerk, though he's still not entirely certain how this happened. Since Fred's not metallic and not used to being on his own, the gang manage to overtake him with ease. This only makes his hatred for the gang grow.

Fred is placed in a cell in the Cooper Gang's safehouse that's made entirely of metal to ensure that his claws can't break through the walls. Fearful that Fred may become Clockwerk, Sly asks Bentley to put a failsafe into the time machine so that nobody but the Cooper Gang can use it, which Bentley does. A few months pass with Fred in captivity, and the thieves grow a little careless, leaving the time machine (which no longer needs an object to travel through time) a little to close to the bars on his cell door. Fred, by planting his feet together, is able to reach his wing through his cell and grab it. He desperately tries to get it to work, but Bentley's failsafe doesn't allow him to. Hearing footsteps and growing desperate, Fred smashes the time machine on the ground, deciding that if he couldn't use it, nobody could.

As soon as it broke, a rip in the space time continuum opened up in his cell, sucking him in. It also tore down the walls and bars, flinging everything it's sucked up into the prehistoric era. Finally free, Fred, realizing he won't be able to kill Sly if he remains in this time period, at first tries to rebuild the time machine, but his efforts are in vain. Instead, he focuses his efforts on prolonging his life, encasing his body in the metallic wreckage from his cell, and even creating a hate chip to ensure that when he reached the present day, he would still have that hatred towards Sly Cooper. He also decided to rename himself Clockwerk, as that was more menacing, and he no longer wanted to be Fred.

The reason I came up with this was because I feel like it makes a lot of sense. It explains why, through his hatred, he never killed the Coopers, or at least allowed them to have children first: so that he could eventually meet up with Sly to kill him himself. It also explains why he left Sly alive when he killed his father. Sure he gave an explanation in the game, but isn't he built out of revenge? He wanted a fair fight to prove he was better than Sly, taking the Thievious Raccoonus as an afterthought. It also explains why he kidnapped Carmelita in the first game and how he knew that she could lure Sly into his trap. And it shows why, in his Thieves in Time cameos, he watches the Coopers instead of interfering and trying to kill them. If you spot any inconsistencies with this and the canon series, let me know. I either overlooked it or forgot to tell that part. Otherwise, let me know what you think!