After you defeat the Cyclops in the Nutripils Factory, go back to the dock, get in the hovercraft and enter the Elevator Room from the water tunnel. There you can now pick up the Pearl.
Here's Beyond Good & Evil - Walkthrough (Gamecube, PS2, XBOX, PC) from IGN.com.
Beyond Good & Evil is a 2003 cult classic. It's a Zelda-style adventure about a photojournalist uncovering secrets on a strange alien world.
The long-awaited sequel to Beyond Good & Evil is indeed real! Ubisoft just released a surprise cinematic trailer for the game at the publisher’s E3 keynote. Find out more at The Verge.