This older generation Di2 wire harness comes with two e-Tube (EW-SD50) electric wires permanently attached to it and one e-Tube port meant to connect to your Junction B (SM-JC40/41) using an additional EW-SD50 electric wire. The wire harness also includes a battery charge indicator.
You'll find this on older bikes only. It does not have a charge port, so it can only be used with the external battery. The lack of a charge port also means you cannot use the SM-BCR2 charger/pc interface to update firmware.