Alpha Team's Mission Deep Sea was released was the second theme released after the unnamed theme a year later in 2002. This subtheme took the characters into the depths of the ocean. The sets focused on vehicles and mutant animals controlled by Ogel, the evil villain. The Alpha Team sets maintained a fleet of underwater vehicles including the Alpha Team Aquatic Mech, a large undersea robot operated by Dash. Set 4795, Ogel Underwater Base and AT Sub, was the first set to have both heroes and villains in it.
Four polybags representing small aquatic vehicles were also released in the Mission Deep Sea subtheme which included set 1425 Jet Sub, 1426 Alpha Team Wing Diver, 1427 Ogel Underwater Slizer and 4799 Ogel Drone Octopus. Later in 2003, two Alpha Team sets were released, both polybags including set 3391 Dash, and a clock, 4193351 Alpha Team Mission Deep Sea Clock.
LEGO released the Alpha Team in 2001 which was initially based on the video game LEGO Alpha Team and discontinued the theme in 2005. The theme centers around a team of secret agents known as the Alpha Team, and their efforts to stop the nefarious villain Ogel from taking over the world which initially ran from 2001 to 2002.