Ah, that's an interesting question.
How does the fangame compare to its replacement... the short answer is that it doesn't - the guy who was writing the plot for KQ2.5 had some real life issues to take care of, which caused him to leave the project before he could actually share his plot with us. So the general plot, puzzles or items weren't unchanged, they had to be rewritten from scratch.
The original plot, or what I know of it, did contain e.g. a monk (who was evil, however) and the chancellor (who was instead an evil vizier, and the main source of trouble). On the other hand, it did not have e.g. Geraint (he was just a regular soldier) or Ashe, and as I recall there were no female characters other than Valanice.
Maeldun is indeed a replacement for Graham, although I believe that Maeldun has more of a backstory than Graham does (in the games, that is; I have never read the KQ novels).
Of course there would have been a number of cameos, for instance my intent was for Graham to take Ifnkov along as his advisor. In particular, as I recall, our writer wanted to join the KQ9 writing team, and have the metaplot that Manannan would stage the events in KQ2.5 to lure Graham out of Daventry, so that Manannan could kidnap Graham's child. The reason why Manannan would do this (or indeed, why he couldn't do it with Graham present) was to be explained in KQ9.
For what it's worth, the short KQ2.5 demo is available on our website. It does not, however, contain any references to the plot, because we didn't know it then.
And on a completely unrelated note, the name Carbonek stems from Arthurian mythology, which explains its presence in ATOTK. I would assume that its presence in Gobliiins is an inside joke. ATOTK intentionally takes influences from mythology, and that includes most of the names. I like to say that the game is a fairy tale, and indeed this is the main reason why it contains a sleeping princess near the end.
I hope that answers your questions
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= Radiant =
