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In the PC version the price the Melnorme ask for the information on why their bridge just turned purple is 120,000 Credits. In the 3DO version and in The Ur-Quan Masters, it takes 12,000,000 Credits. In no version can you actually acquire the required amount of Credits.
The Melnorme speak of this artifact in the PC version. It isn't mentioned in the 3DO version or in UQM.
The size of the cargo hold of the Planet Lander
In the PC version, the Mycon mention the location of their homeworld in several conversations. In the 3DO version and in UQM they don't.
Buying a Syreen Penetrator
In the PC version, you had the option of filling a Penetrator's crew to its peak of 42 crew from your Starbase.
The PC and 3DO version would never have Slylandro Probes in star systems, but UQM it can happen. The PC and 3DO version did contain code intended to make it possible, but due to a bug it did not work. In UQM the bug is fixed.
The Ur-Quan Masters is the only version of Star Control 2 that supports SuperMelee games over a network.
The PC version of Star Control used a 320x200 screen resolution. The 3DO used 320x240, but had large borders around the edges, (for better viewing on TV screens), which meant the usable space was even less. UQM uses 320x240 internally, without the large borders, and has several scaling methods available to improve the quality on higher resolutions. 640x480 mode is available in pure SDL mode, higher resolution modes are only available in OpenGL mode.
On the PC, you could review your conversation partner's words in dialogs when it was your turn to speak. The 3DO version instead had a progress bar for the spoken text. You could rewind and replay this text, even as it was being spoken. UQM has both.
The game menus in the PC version were purely textual, with the various choices visible at once. On the 3DO, with text on a TV screen being more difficult to read, only the current selection was visible, in the form of an image with some text above it. In UQM you have the choice. Up until version 0.3 the default was 3DO menus, after that, the default is PC menus.
On the PC, the planet statistics were described in text. On the 3DO, where this was harder to read, Toys for Bob have chosen to replace this text by images. In UQM you have the choice. Up until version 0.3 the default was 3DO images, after that, the default is PC text.
In the PC version, when you landed on the surface of a planet, you could only see the surface directly around the lander, in a small box in the bottom right corner of the screen. On the 3DO the entire main window was used for this. UQM does it like the 3DO.
Intro and ending
The PC version had a slideshow intro and ending, whereas the 3DO version had pre-rendered 3d cutscenes. Due to copyright issues, the 3d movies can't be distributed with UQM, but the current CVS version of the game is able to play them if you have the original 3DO CD to extract them from. More information about this can be found here. The PC slides are available in version 0.4 and higher. The 3d cutscenes and 3d ship description videos were created by PCA Graphics (see also their Star Control II gallery).
Ship animations in super melee
In Super Melee the 3do had animations for each of the ships. Due to the same copyright issues as with the intro and ending videos, these can't be distributed with UQM either. It is currently not even possible to use these movies in the game even if you have extracted them from the 3DO CD yourself. This should change in the future.
The music of the PC version was solely tracker music. In the 3DO version, the orbit and solarsystem music were freshened up, the battle, HyperSpace, Starbase, outfit flagship, and shipyard music were remixed, the QuasiSpace music was replaced, 4 new orbit tracks were added, and the intro, victory and credits music were replaced by the background music of the new videos. For UQM you can enjoy either version. The music from the PC version is contained in the main content package; the 3DO music is available in a separate package. In addition, you may download music specially remixed for UQM by the Precursors.
Unlike the PC version, where all dialogs were shown as text, the 3DO version contained spoken voice for all the alien dialogs (about 12 hours in total). There are some small discrepencies between the two, as shown here. In UQM, the dialog text matches the 3DO words, with the actual speech being in an optional package (about 110 MB in size).