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- Rattrap salvages a computer bank from the Axalon and in it's circuits he and Rhinox find the core consciousness of the old Dinobot (which as you will recall Dinobot downloaded in a previous episode). Rattrap gets obsessed with the idea that he can restore the old Dinobot by getting it into the new Dinobot's systems. Rhinox tells him this will probably not work, as a core consciousness without a spark is only an illusion of the person to whom it belonged. And if it didn't work, it just might give the Dinobot II all the old Dinobot's memory schematics and habits on the Maximals which could give the Preds and advantage. Optimus thus forbids the attempt. Rattrap defies this order, sneaks out and at much risk to himself, does manage to get the core consciousness in place. For a moment the old Dinobot does seem to emerge but as Rhinox warned he is only a shadow of his former self and must do everything he can to keep Dinobot II from regaining control of his body, a weird mental struggle which would have been fun to animate. The old Dinobot knows he is doomed to lose this struggle and tries to "sacrifice" himself again by infiltrating the Predacons and taking out Megatron before he can complete his master plan to destroy the Autobots that were in stasis in the Ark. It doesn't work and Dinobot II regains control of his body only to be blasted by Megatron. Rattrap comes to accept that his old pal is truly dead and realizes he cannot bring him back. However he honors his friends memory. (original post)
Details of rejection
Word that the "Dark Glass" script had been rejected reached the fan community before the third season of Beast Wars even began airing. Rumors ran rampant that the script had been rejected for being "too dark", and this account was seemingly confirmed by DiTillio in a 1998-Aug-10 post to ATT  and by Marx in a 1998-Nov-16 post to a Jem mailing list. 
Several months later, on the same day that Palaste posted the plot summary, Jon Hartman also posted to ATT to say that Claster, the series distributor, had rejected the episode because the story did not have enough action . This statement is in moderate conflict with the earlier statements by parties closer to the events in question, but grimness and a lack of action could certainly go hand-in-hand. Additionally, Claster at this time was a subsidiary of Hasbro, so it possible that Hartman's claims are simply a more detailed description than had been provided by DiTillio or Marx.
- Q: Is it true that there was to be an episode called "Dark Glass" in season 3, but refused production by Hasbro?
- A: No, this is actually not true. "Dark Glass" was rumored as a lost episode that was to feature Rattrap attempting to restore the original Dinobot's personality to Dinobot 2, and that when the episode was refused, "Go With the Flow" was made instead. The truth is that "Dark Glass" was written for season 2 and rejected by the story editors, not Hasbro, because the script was not up to standard. The script was replaced by "Transmutate", a great episode that was a better fit for season 2."
Given that eight years had passed when he said this, it is likely that he misremembered the sequence of events. This account contradicts statements by himself and Marx, a sneak peek at the episode list for season 3 seen at Botcon 1998, and the confusion surrounding the failed distribution of the script at Transcon III (see below). Therefore, the DVD account should be taken quite skeptically.
Availability of the script
Although the episode was dropped from the schedule long before any animation or voice recording would have been done, the "Dark Glass" did have a full first-draft script written by Marx, which was then rewritten once by DiTillio, as stated in his post from 1998-August-10.
On 1998-Aug-29, just a couple weeks after DiTillio explained the rejection, toy dealer Dennis Barger of Men In Black Collectibles -- the organizers of BotCon 1996 -- posted to the thread to announce that he had acquired a copy of Marx's script from her. For his upcoming unofficial convention, Transcon III, he planned to place the original in a charity auction, and distribute reproductions to all attendees.  Hearing concerns from fans, Barger later stated that he would have all recipients of the script sign non-disclosure agreements to prevent spoilers from being leaked until the third season had aired.  (Transcon III was to take place in September 1998, while season three wouldn't even premiere until October.) However, as stated in Marx's Jem list post, and later summarized on ATT by Rob Powers , Barger had not obtained the proper approvals from Hasbro and/or Mainframe, and the whole affair fell apart. The script was returned to Marx. Furthermore, Mainframe decided that no scripts were ever to be released to the public again, and indeed, although scripts for seasons one and two of Beast Wars were available on Ben Yee's website, those for season three and Beast Machines were never put up. 
There was a sizeable interest in the script from fans, and Dave "Zobovor" Edwards even gathered over 500 signatures to a petition for the script's release, but he never received a response and by September 1999, he threw in the towel. 
Fans have extrapolated that this episode would have explained Dinobot's re-emerged personality in the show's final episode, "Nemesis Part 2".
In that episode, Rampage, whose spark powered the Transmetal II clone of Dinobot, was killed, and his spark extinguished. At the same time, Dinobot II suddenly seemed to remember the last moments of the original Dinobot, and his behavior changed drastically; speaking of honor, he defied Megatron and essentially switched sides (before dying again).
These events are difficult to explain, perhaps especially so without "Dark Glass". The Dinobot II body was a clone of the original Dinobot, but did not (as far as is known) possess his core consciousness, memories, engrams, etc. Rather, Dinobot II seems to have been a shell program written by Megatron running on top of a fragment of Rampage's spark. In this case, it is unclear why, in the absence of Rampage's spark, Dinobot II would suddenly act more like Dinobot I. However, if the events of "Dark Glass" are taken to have occurred off-camera, it becomes easier to understand: two shell programs and a spark all fighting for dominance over a single body. With the spark gone, the Dinobot I shell may have had an opportunity to take over.
On the other hand, even with "Dark Glass", the picture is incomplete. Dinobot saw visions of the original Dinobot's last moments, his battle with the Predacons in the rift valley at the end of "Code of Hero". These memories could not have been part of the download Dinobot made into the Axalon's computer earlier in the season. For them to surface within him, they must have either been added to the datatrax he was programmed with (by either Megatron or Rattrap), or they must have come from Dinobot's own spark, if that spark somehow left the Allspark and inhabited the cloned body when Rampage's spark departed. All three of these possibilities have their share of implausibility, so it is up to each fan to pick an interpretation that they like to include in their personal canon.
- The concept of this episode would later be used when Rattrap unlocks Rhinox's memories in Tankor. It will not turn out in Rattrap's favor.
Reference posts, sorted by date
- DiTillio, 1998-Aug-10 - Description of the rejection.
- Barger, 1998-Aug-29 - Announcement of availability at Transcon III.
- Barger, 1998-Aug-29 - Non-disclosure agreement mentioned.
- Marx, 1998-Nov-16 - Description of the rejection, mention of the Transcon III auction and the return of the script.
- Palaste, 1999-Feb-17 - Summary of episode as described by DiTillio.
- Zobovor, 1999-Sept-20 - Final status of petition to release the script.