Book of Insight
The Book of Insight is accessible between Campaign missions. In it you can spend Knowledge Points on skills. Skill can improve units or the citadel, unlock new pieces or give new passive or active abilities to Iris. Purchased skills can be refunded at any point.
Certain skills require a higher Expedition Level before they can be unlocked. Level II (Prodigy) requires 5 Knowledge Points and Level III (Master) requires 10 Knowledge Points.
The Book of Insight is not available in other game modes. In Skirmish and Sandbox everything is unlocked while in Endless skills are bought using points instead.
Citadel
Citadel skills improve the citadel.
Units
Units skills improve the attacks of one the units.
Pieces
Pieces skills unlock new pieces.
Iris
Iris skills improve Iris' capabilities and unlike other skills they come in mutually-exclusive groups of two as well as two levels each.