Powering LEDs using transistors controlled by arduino mega

Why are you powering the LEDs from the emitter, that is a bad way to do it. Usually it is like this:
Vcc
Z
Z
|
x------------(Out to LEDs)
|
| /
o---VVV------| (NPN)
|
v
|
Z (only needed to limit current, otherwise emitter to GND)
Z
|
GND

Made an Edit, added missing resistor to collector