I doubt you'll be able to get through the Pirate talk for now, but this is the classic 'Red-alert' bug. If I'm not mistaken, you'll need to do some minor FRED work to get around it (I did) or I can once I get home and determine exactly what mission you're talking about since the Pirate talk is kinda in the way. Other potential solutions would be to replay the previous mission a few times, or maybe try making a new pilot.
Naturally I'm not sure how familiar you are with messing around in a PC's directory structure, but if you're game for the FREDing way:
Check out the Wiki for modding tools (or otherwise find VPView or maybe VPMage) and use one to open the .VP file and extract the appropriate .fs2 mission file to the \data\missions\ folder (or [modname]\data\missions if applicable) You may have to create those folders yourself either way.
I can't seem to type that without making it sound overly complicated... not wot th' bleedin' scurvy Pirate talk be helpin' it much, thar laddie.
Anyway, launch FRED from the 'root' Babylon folder, browse to where you extracted the .fs2 file and open the mission. Once there, assuming all goes well, go to editors->mission specs and look at the top right of the window that opens. Uncheck 'red-alert' mission and then save and exit. Launch TBP and revel in your awesomeness at fixing the problem!