This requires plasma charge. An easy way to beat Lightning is when she says "Come my children" or when she says "Kill him!"
After monsters climb on the train, she should come down to be vulnerable. Attack the boss with the plasma charge, then when you have your spirit gauge full, she will make rake lightning across the train.
Keep up the attack pattern and when she says "My power is gone", you can approach and press the L1 button to finish her.