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Topos is an open interoperability protocol designed to reduce as much as possible trust assumptions by replacing them with cryptographic constructions and decentralization while exhibiting massive scalability. The protocol does not make use of a central blockchain, nor uses consensus to ensure consistent delivery of messages across a heterogeneous ecosystem of public and private blockchains, named subnets, but instead relies on a weak causal reliable broadcast implemented by a distributed network which we call $\textit{Transmission Control Engine}$ (TCE). The validity of cross-subnet messages is ensured by the $\textit{Universal Certificate Interface}$ (UCI) and stems from zkSTARK proofs asserting the validity of subnets' state transitions executed by the Topos zkVM. Such proofs of computational integrity are publicly verifiable by any other participants in and out the protocol such as other subnets or audit companies. The interface between the TCE and subnets leverages the ICE-FROST protocol, an innovative threshold signature scheme, whose static public key allows for uniquely identifying subnets after they register in the protocol. The Topos protocol is designed to provide $\textit{uniform security}$ to the ecosystem and to handle any type of subnets (e.g., permissioned, permissionless) in order to fit any business use cases and pave the way for global adoption and a new standard for the Internet base layer.