This brings back a lot of memories. It is a shame that this seems it will never be finished. We can only speculate where the story could have gone. I do have a few theories based on the diaries and whatnot...
Theory #1: Rufus is an alternate version of the old man. This might better explain how he knows the secrets like the Chronoplast. It is possible Rufus is a disgruntled version that no longer wanted to uphold the stream of time...
Theory #2: Rufus is an alternate, time-displaced version of the Old Man's son. TOM mentioned he feels familiarity around Rufus, and finding out Rufus' betrayal broke his heart... It would be interesting to hear Rufus' motivation in this case. I don't think it's as touching as "I want to free my dad from his job."
Theory #3: Pliskin is an alternate time version of Rufus. It's a sort of trope guess at this point. There's not much support for this, but it would be interesting if that is what Rufus meant by how well he knew Pliskin.
Theory #4: Pliskin is an alternate time version of the Old Man. This isn't too likely, but Pliskin and the old man are both Timestreamers and it could be foreshadowed in the diary where TOM believes he is the only one who can defeat Rufus...
All in all, a few new characters like Jessup and his crew get introduced here, but don't get a lot of development. The gameplay is a bit repetitive when you have to click the items over and over again to interact with them in different ways. I liked the 2nd part a bit better, though the art and animation were not as good as part 3.1. Still, this is a fond memory of the flash days for me.