The practical construction of scalable quantum-computer hardware capable of executing nontrivial quantum algorithms will require the juxtaposition of different types of quantum systems. We analyze a modular ion trap quantum-computer architecture with a hierarchy of interactions that can scale to very large numbers of qubits. Local entangling quantum gates between qubit memories within a single register are accomplished using natural interactions between the qubits, and entanglement between separate registers is completed via a probabilistic photonic interface between qubits in different registers, even over large distances. We show that this architecture can be made fault tolerant, and demonstrate its viability for fault-tolerant execution of modest size quantum circuits.