Adventure Mode: The Subspace Emissary

 The Subspace Emissary is the Adventure mode in Super Smash Bros. Brawl. It mainly involves the assorted Nintendo characters' struggles against the Subspace Army.

Samus Aran's involvement begins when she infiltrates the Research Facility on the Isle of Ancients as Zero Suit Samus. After working her way through part of the facility and defeating the various R.O.B. sentries she encountered along the way, she discovers a trapped Pikachu that is being drained of its electricity; once Samus frees it, the Pikachu teams up with her for much of the remainder of the Subspace Emissary. After defeating the R.O.B. sentries that responded to the alarms set off by Pikachu's release, Samus and Pikachu make their way further into the Research Facility, where they eventually find a screen displaying Samus' Power Suit that is being held elsewhere in the facility, presumably while being studied.

Zero Suit Samus and Pikachu make their way to the chamber where the Power Suit is being held; before Samus can recover it, however, two darker versions of her Power Suit attack the duo. After defeating the two "Dark Samuses", Samus dons her Power Suit; beyond this point, it seems to be impossible to play as Zero Suit Samus for the rest of the Subspace Emissary. With her Power Suit recovered, Samus continues working her way through the Research Facility with Pikachu in tow. Some time later, the two are ambushed again, this time by Ridley. After defeating her arch-nemesis once again, Samus discovers two R.O.B.s transporting a Subspace Bomb from another area of the Isle of Ancients; presumably, she began investigating that area as well.

Later, Samus' storyline is revisited as she infiltrates the Subspace Bomb Factory along with Pikachu. After going through part of the Factory, they confront the Ancient Minister, who does not attack them. Shortly afterwards, Captain Falcon, Captain Olimar, Donkey Kong, and Diddy Kong all arrive, having entered the Factory via a different route. Samus is present when the Ancient Minister reveals himself to be R.O.B. in disguise, prompting an attack from Subspace forces under Ganondorf's command. After the battle, Samus and the rest must escape before the Subspace Bombs explode, so they make their way to Captain Falcon's Falcon Flyer. While flying out of the Isle of Ancients, however, the group is ambushed by Meta Ridley and must defeat him in 2 minutes.

When the Subspace Gunship appears, Samus' gunship is one of the vehicles seen entering the portal to Subspace. Samus is one of many characters that travel through Subspace to confront the Master Hand. She is present when Tabuu reveals that he has been the one pulling the strings -- literally -- during the entire Subspace Emissary. Samus, along with everyone else, is subsequently turned into a trophy by Tabuu's Off Waves and is revived by Luigi, Ness, and King Dedede. Finally, Samus is one of the characters to make it through the Great Maze and confront Tabuu at the end. She is last seen standing on a promontory with the rest of the characters looking at what remains of the Isle of Ancients.