To get the clear "crystal" (gem), what you have to do is just before the section where you
have to throw Cortex to activate the 3 switches, keep walking after the 2 hot bars. Get
onto the platform, and throw Cortex so he hits the "!" crate. This will activate a bridge
of steel crates which you walk across to get the gem.

Just make sure you wait for him to return to you before you walk out to get the gem - or
he will reappear below you - at the start of the level.