Jake (John in the Japanese version) is hired as an apprentice magician by Zebedia Pong (simply referred to as Pong in the Japanese version). He is training when some strange people attack and kidnap his girlfriend, Allison (Yuu in the Japanese version). Jake goes on a quest to find out where they came from and why they wanted Allison. Afterwards, Jake discovers Allison's kidnapping was a feint to force Allison's father, a renowned scientist, out of hiding. Jake must not only save Allison's father, but ultimately battle an evil king who plans to lead a group of underground-dwelling people in a battle against the people of Jake's world.

The Japanese and North American versions of the game are mostly the same, except for the characters. In the original Japanese game, the main characters are two anime-style friends who happen to be pre-teenagers. In Totally Rad, they are redesigned into becoming two Californian teenagers who constantly talk using "surfer" lingo from the 1980s. Since most people start having boyfriend-girlfriend relationships as teenagers in North America instead of as pre-teenagers, the characters of Jake/John and Allison/Yuu were "aged" approximately five years.

The instruction manual for Totally Rad is filled with surfer talk and lingo, in addition to comical picture breaks and comments about the author's "babe" and how attractive she looks in the picture he put of her in the instruction manual.