Metroid II: Return of Samus. The story follows Samus as she hunts down the Metroids on their home planet. It's a story of survival and exploration in a hostile alien environment. The isolation of Samus and the sense of danger add depth to the story.
One that shouldn't be overlooked is 'Advance Wars'. The story might seem simple at first, but as you get into the game, you realize how it ties into the strategic battles. You have different commanders with their own motives and the story of the war between the Orange Star, Blue Moon, and other nations is quite interesting. And of course, 'Pokémon Emerald' has a lovely story with lots of heart, especially when it comes to the bond between the trainer and their Pokémon.
One great example is 'The Legend of Zelda: The Minish Cap'. It has an engaging story where Link shrinks down to the size of a Minish to save Princess Zelda. The adventure involves exploring a detailed world filled with unique characters and quests.
A really good one is 'Pokémon Ruby/Sapphire/Emerald'. The story of becoming a Pokémon master, stopping Team Magma/Aqua from their evil plans, and exploring the Hoenn region is full of charm. There are also the relationships between your Pokémon and the other characters. 'Mario & Luigi: Superstar Saga' is also great. The story of Mario and Luigi going on an adventure to save Princess Peach's voice from the evil Cackletta is hilarious and full of fun gameplay elements related to the story.
Final Fantasy Legend III also has an excellent story. It has a complex plot with time - traveling elements. The characters are on a quest to save their world, and as they progress, they face various challenges and revelations. The story is full of twists and turns that keep players hooked from start to finish.
One popular 'gameboy advance visual novel' is 'Phoenix Wright: Ace Attorney'. It features engaging courtroom battles and a great storyline. Another is 'Hotel Dusk: Room 215' which has a unique mystery - solving element with its noir - like atmosphere.
I'd say 'Crisis Core: Final Fantasy VII'. It has a heart - wrenching story that fills in a lot of the backstory for characters like Zack Fair in the Final Fantasy VII universe. You get to see his relationship with Cloud and his journey within Shinra. 'Daxter' is another good one. It follows Daxter as he tries to rescue his friend Jak. The story is full of humor and action as Daxter takes on various jobs and battles enemies in a world full of strange creatures. 'Resistance: Retribution' also has a solid story. Set in an alternate - history world where the Chimera are invading, you play as a soldier trying to fight back and uncover the secrets behind the invasion.
Portal 2 has an excellent story. It's a puzzle - based game where you use a portal gun to solve various challenges. But the real charm is the story that unfolds as you play. The humor, the mystery behind the Aperture Science facility, and the relationship between the characters like Chell and Wheatley make it a memorable experience.
Cyberpunk 2077. Despite its initial glitches, it has a great story. It's set in a futuristic, dystopian world of Night City. You play as V, and the main story arc along with the side quests are filled with interesting characters and plotlines that explore themes like identity and power.
Detroit: Become Human is quite popular. It's an interactive drama where your choices shape the story. You play as multiple characters, each with their own story arcs in a world where androids are becoming self - aware. It offers a unique storytelling experience with different endings depending on your decisions.
One game is 'Final Fantasy VII'. It has a story that combines elements of fantasy, science fiction, and environmentalism. The story of Cloud and his fight against the evil Shinra Corporation is iconic. It also has a great cast of characters, each with their own backstories and development throughout the game.