The spent alien power cell will appear dimmer when reloading, as if drained of power. With Mothership Zeta installed, the Lone Wanderer will be abducted before being able to pick up the alien blaster from the crash site, though it can be picked up after they return.
The alien crash site is found due north of MDPL-13 power station and northwest of the Greener Pastures disposal site.
The alien blaster can be found next to the body of a dead alien lying a few feet away from his crashed spaceship.