If I remember correctly, this will happen 4 times:

1. Appease or anger the Protoss (the one the TS is talking about)

2. Protect the Terran settlement or let the zerg have their way

3. Ally with Tosh or Nova (this is where you get to choose between the Spectres or Ghosts)

4. Destroy the Nydus network or the spires (which will culminate in how you want the last mission to be: vs ground units or vs air units)

Regardless of what you choose though, as soon as you finish the mission of your choosing, the alternate mission will be unlocked for you to play through so you could still earn the achievements on it.