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The quantum logic gates used in the design of a quantum computer should be both universal, meaning arbitrary quantum computations can be performed, and fault-tolerant, meaning the gates keep errors from cascading out of control. A number of no-go theorems constrain the ways in which a set of fault-tolerant logic gates can be universal. These theorems are very restrictive, and conventional wisdom holds that a universal fault-tolerant logic gate set cannot be implemented natively, requiring us to use costly distillation procedures for quantum computation. Here, we present a general framework for universal fault-tolerant logic with stabiliser codes, together with a no-go theorem that reveals the very broad conditions constraining such gate sets. Our theorem applies to a wide range of stabiliser code families, including concatenated codes and conventional topological stabiliser codes such as the surface code. The broad applicability of our no-go theorem provides a new perspective on how the constraints on universal fault-tolerant gate sets can be overcome. In particular, we show how non-unitary implementations of logic gates provide a general approach to circumvent the no-go theorem, and we present a rich landscape of constructions for logic gate sets that are both universal and fault-tolerant. That is, rather than restricting what is possible, our no-go theorem provides a signpost to guide us to new, efficient architectures for fault-tolerant quantum computing.