Well I penetrate inside the giant cell as the first organic stage in Gradius series, where Amoebas are first appeared. And there's no sub-boss but the near-end boss is called the nucleus.
Title(s): Nemesis (International title), Gradius/グラディウス (Japanese title)
BGM(s): Beginning of History + Mechanical Globule (the 6th stage theme) + Aircraft Carrier
Composer: Miki Higashino (東野美紀)
Last recorded: September 26, 2014
Player: Axl
