Voici les différents parcours à suivre pour obtenir les 9 fins du jeu. D'autres possibilités existent, mais les parcours indiqués vous permettent de débloquer toutes les missions. Les choix à faire sont proposés entre crochets. A noter que la difficulté augmente à chaque fois que vous terminez le jeu.

Fin 1 : Fox and Krystal

The Adventure Begins (Corneria), [contact Slippy] Reunion with Slippy (Corneria), [set course for Fichina] Fog of War (Fichina), [gather intelligence] Missile Threat (Asteroid Belt), [say good-bye to Fox] Hold Firm, Katina ! (Katina), The Worm (Titania), Fox and Krystal (Venom).

Fin 2 : Good-bye, Fox

The Adventure Begins (Corneria), [contact Slippy] Reunion with Slippy (Corneria), [set course for Fichina] Fog of War (Fichina), [fight Oikonny] Oikonny Strikes Back ! (Fichina), [check out Corneria] Father and Son (Corneria), [head for Titania] Andross's Legacy (Titania), Good-bye Fox (Venom).

Fin 3 : The Anglar Emperor

The Adventure Begins (Corneria), [contact Slippy] Reunion with Slippy (Corneria), [set course for Fichina] Fog of War (Fichina), [fight Oikonny] Oikonny Strikes Back ! (Fichina), [go to Amanda] Beneath the Waves (Aquas), We Meet Again (Sector X, Y, Z), The Anglar Emperor (Asteroid Belt).

Fin 4 : Star Wolf Returns !

The Adventure Begins (Corneria), [attack advance guard] Decision Time (Corneria), [meet up as planned] The Meteorite Trap (Asteroid Belt), Octoman's Ruse (Aquas), [bring her back] Krystal (Katina), [leave without Fox] Star Wolf Returns ! (Venom).

Fin 5 : Lucy and Krystal

The Adventure Begins (Corneria), [contact Slippy] Reunion with Slippy (Corneria), [set course for Fichina] Fog of War (Fichina), [fight Oikonny] Oikonny Strikes Back ! (Fichina), [check out Corneria] Father and Son (Corneria), [say farewell to Peppy] Lucy and Krystal (Corneria).

Fin 6 : Dash Makes a Choice

The Adventure Begins (Corneria), [attack advance guard] Decision Time (Corneria), [go to Fichina instead] Former Rivals (Fichina), The Red-Hot Planet (Solar), The Ultimate Weapon (Solar), [sorry, I'm out of here] Dash (Titania), Dash Makes a Choice (Venom).

Fin 7 : Slippy's Resolve

The Adventure Begins (Corneria), [contact Slippy] Reunion with Slippy (Corneria), [locate Peppy first] General Peppy (Corneria), [join the hunt on Aquas] Amanda (Aquas), Slippy's Resolve (Aquas).

Fin 8 : Pigma's Revenge

The Adventure Begins (Corneria), [where is Falco ?] Falco to the Fore ! (Katina), Falco's Decision (Asteroid Belt), [search for Krystal] Pigma's Revenge (Sector X, Y, Z).

Fin 9 : The Curse of Pigma

The Adventure Begins (Corneria), [attack advance guard] Decision Time (Corneria), [go to Fichina instead] Former Rivals (Fichina), The Red-Hot Planet (Solar), The Ultimate Weapon (Solar), [let's find that weapon !] Wolf's Plot (Titania), [go after Fox] The Curse of Pigma (Sector X, Y, Z).