the real confusion comes when you dont realise that the transistor doesnt actually amplify anything !!
a NPN transistor is like a valve ( water/or gas), the base of the transistor is the valve control
by varying the size of the small current to flow between the base and emitter, it controls a larger
current that can flow between the collector and emitter ....
so for example on a power transistor ... you may have 1mA flowing between the base and emitter and this allow 1 Amp (1000mA) to flow between the collector and emitter
increase the base current to 10mA and you will allow 10 Amps to flow between the collector and emitter
The appearance of amplification is given, BUT there is NO actual amplification as such. Just a varying small current flow controlling a larger current flow
hope that helps
Dave