First, before patching i would copy Uni_7BattleGrave.scr and save it in a separate directory.
then I would DL and install patch 2036, then take the script you just copied and replace the one the patch put in.. for some reason, the patch bugges that mission..
then i would replace your desktop icon with a new shortcut pointing directly to the Starfleet2.exe game file to bypass the intro movies.. the intro movies bugg fighters and shuttles in game.
then in your mission as stated above, after beaming down the ambassador using your little transporter icon (not the Icon near the top right of your command console, but the lower left side of your console where your weapon status is located), 2 ISC and an Organian arrive.. I suggest crippling one ISC and capturing it, then destroying the other.. ou get Astounding Victory for doing this.. but make sure to use your Comms Channel and do dialogue with all the ships at the beginning and middle of your mission (when approaching the planer, then again when the ISC arrive and make their Ultimatum.. contact all non ISC ships first to make alliance then contact the ISC then the Organian).. also make sure to beam your Diplomat back to the ship just after the ISC arrive, but before engaging them in combat.
Hope that this helps.