On most missions of the game, there is an alternate route that can be reached at the end. These usually require fulfilling special obligations. If these are not met, then the "default" mission will follow.

Mission	How to unlock
Aquas	Shoot down at least 100 enemies on Sector Y.
Area 6	Can only be accessed through accomplishing the missions on either Sector Z or Macbeth.
Katina	Fly through the seven warp rings in Meteo; or reach it from Sector Y.
Macbeth	Defeat Spyborg on Sector X before it knocks out Slippy; or reach it from Solar or Zoness.
Sector Y	Save Falco and fly through the stone arches on Corneria.
Sector Z	Fly through the warp gates on Sector X; or reach it from Zoness.
Solar	Shoot down the Star Wolf team on Fichina before the bomb explodes; or reach it from Katina.
Venom (2)	Can only be reached from Area 6.
Zoness	Can only be reached from Aquas.