The original Zybourne Clock was intended to be 100 hours long, but in fact, they were pretty much just two separate games that are united together only by a shared storyline. Act 1 of the story was 50 hours long (including sidequests) and focus around Sylus, and Act 2 would be another 50 hours long (including sidequests) focusing on Sam McLaughlin. Add them together, and you get 100 hours.
But what is this storyline? Allow me to summarize it with a timeline helpfully provided by one of the original artists of this game.
Shii: "During the biggest Something Awful thread one of the original Zybourne Clock artists came in and posted this. He quit the project before the "developers" decided to include it, but consensus says it is definitely canon."

If you had read the previous two chapters I written, you know what Timeline 1 was all about...the perpetual civil war that ended when Dr. Zybourne developed and sent his clock back in time. Included with the clock is a failsafe; if the clock detects that humanity has a theoretical chance to tamper with it, the clock will send a distress signal for help. To further protect the clock from tampering, several people were sent back in time along with the clock to protect it from being tampered.
Act 1 takes place in the Timeline 2 created by Dr. Zybourne. The insertion of the Clock sped up human evolution...but
the people sent back to the past posed a problem. Those people established a religious sect, The Order, to protect the clock from tampering, but somewhere down the line, The Order's original mission slowly morphed from "Stop the world from ending" to "Destroy this sinful earth by causing armageddon, thereby paving the way for an ascension of the faithful". And remember, timelines do not get overwritten, so Dr. Zybourne still exist, only now, he's the one actually leading The Order by the time of the game's start, under the alias of "The Prophet".
Sylus is an R&D scientist who is being groomed to take over The Order after Dr. Zybourne dies...which is problematic for Sylus because he considers himself a 'true atheist' and a staunch opponent of organized religion. Nevertheless, Sylus organized a band of merry followers, including Johnny Five-Ace. Together, they went through numerous adventures to track down the Zybourne Clock. Once the party located the clock though, Sylus betrayed the party so that he can secure sole possession over the valuable clock. Sylus successfully killed the entire party...meaning, yes, Sylus killed Johnny Five-Ace.
Sylus went to work modifying the clock and reprograming it to the specifications of The Order...Then Sylus realized that the clock doesn't actually cause the end of the world...or cause an ascension...or indeed do anything at all other than change the Earth's climate. By speeding up the clock's mechanic, the climate of Earth became much more hostile to humanity. Though humans did end up evolving faster, a brutal and bloody civil war started up as the remaining humans fight for scarce resources.
With Sylus' whole world crumbling into pieces, he destroyed the Clock and washed his hands cleaned of the entire pointless affair. This action triggers the 'failsafe' I mentioned earlier, as the clock now knows that it can be tampered with. A distress signal is sent...but to ensure that it doesn't get intercepted by Slyus, the distress signal is sent
back in time, just like the clock is sent back in time. It is delivered to a girl named Sam McLaughlin, who is instructed to prevent the "future" destruction of the clock by whatever means necessary.
Act 2 takes place in the Timeline 3 caused by the clock's distress signal, and honestly, there does not appear to be a lot of detail about this. This makes sense, as planning the storyline of Game II when you haven't even started work on Game I would just be idiotic. However, what I do know is that a major plotpoint would be Sam infiltrating The Order and murdering Sylus. It ends with the clock's destruction being retconned out of existence, so human evolution presumbly proceeds as scheduled.
I...I won't use much of this plot. At all. If I want to make a sequel to "Zybourne Clock Redux", I have an escape clause in the form of the Clock's ready-made distress signal, but I won't mention it in the game. I might carry over The Order, but I don't know how to reconcile it, and in any event, I'm going to change their religious focus.