The Shimano E-Tube SM-BCR2 Battery Charger with charging cord connects to the three or five-port SM-EW90 junction box and charges the internal battery. If you have an External battery, you need the regular external battery charger and the power charger cable. The internal battery requires this charger. Because it plugs into the SM-EW90 junction box, there is no need to remove the battery. The charger has two indicator lights - one indicated charging or a charged battery and the other indicates a problem with the system. As a bonus, you can also use this with a PC (sorry Apple users) to update Di2 component firmware and change system functions.
All Di2 components on the bicycle require the same firmware version. Using Di2 components with different firmware versions may cause malfunctions. Use Di2 system checker to update component firmware from http://e-tubeproject.shimano.com/