In accordance with some embodiments, a first apparatus that provides protocol isolation includes a controller, one or more re-configurable data communication devices operable to provide alternative transport of data for a native data communication device on a second apparatus to an external device, and one or more data converters coupled to the one or more re-configurable data communication devices. The protocol isolation method performed by the first apparatus includes establishing a local communication channel with the second apparatus. The method further includes exchanging the data via the local communication channel with the second apparatus according to a first protocol. The method also includes converting the data to a second protocol different from the first protocol. The method additionally includes exchanging, via a first re-configurable data communication device of the one or more re-configurable data communication devices, the converted data with the external device according to the second protocol.