First run sound3v or another sound driver like jrsound to make the PCjr compatible with Tandy 1000 3 voice sound. Then run Indy3. 

The game is cracked, so when the code screen comes up, just select any three symbols (or four?). (Just keep selecting symbols until the game continues.)

My work here was based on an older patch circulating online for years. However, that patch only allowed 16 colors. It did not allow the PCjr's 3 voice sound, even if you tried to force it with both a sound driver and the game's "ta" command. For some reason, it always reverted to PC speaker. 

So, a little while back, I found a different patched version on Trixter's Oldskool website that didn't patch for color, but did patch to force 3 voice sound by default regardless of the graphics setting. It took me some time, but I managed to alter the 16 color patch to work with his version of the game. That did the trick. Now the game runs in both 16 colors and 3 voice sound on an unmodified jr!