The manipulation of topologically ordered phases of matter to encode and process quantum information forms the cornerstone of many approaches to fault-tolerant quantum computing. Here we demonstrate that fault-tolerant logical operations in these approaches can be interpreted as instances of anyon condensation. We present a constructive theory for anyon condensation and, in tandem, illustrate our theory explicitly using the color-code model. We show that different condensation processes are associated with a general class of domain walls, which can exist in both spacelike and timelike directions. This class includes semitransparent domain walls that condense certain subsets of anyons. We use our theory to classify topological objects and design novel fault-tolerant logic gates for the color code. As a final example, we also argue that dynamical “Floquet codes” can be viewed as a series of condensation operations. We propose a general construction for realizing planar dynamically driven codes based on condensation operations on the color code. We use our construction to introduce a new Calderbank-Shor-Steane–type Floquet code that we call the Floquet color code.