NOTE: The 2.00.03 patch (download link) is the final patch for the 2009 UCCE 2.0 game. It will install over any (regardless of where it was purchased) previous 2.0 version. Though it's better to apply it to a new install of the 2.0 version (2009) of the game.
No further patches will be released for this 2009 legacy product. So, consider this as a gift for your support. :)
All future updates are only for The Lyrius Conflict DLC which only works with the Steam version of UCCE 2.0.
If you have the paid version of the 2009 UCCE 2.0 game, you don't need to buy The Lyrius Conflict if you only want this final 2.00.03 patch. See above.
The standalone 2.00.03 patch for the 2009 UCCE 2.0 does the following:
NOTE: If you installed the full game in your Steam folder so you could run it from Steam, then the patch should work I think. I can't guarantee it though; so you're on your own. You just need to point the patch to the install folder when prompted.
v2.0 (2015) Steam
If you have v2.00.02 version on Steam and you purchase the The Lyrius Conflict DLC, the update does the following:
applies the 2.00.03 patch
adds all the new content unique to the Steam version. See the v2.0 changelog for more info
adds all the on-going v3.0 updates. See the v3.0 changelog for more info
The Lyrius Conflict DLC
This only works with the Steam v2.0 2015 release. It does NOT work with the 2009 paid v2.0. It patches and upgrades to the v3.x game engine and beyond.