Go towards the Eastern exit from the boiler room [Maintenance Elevator Access], reach the elevator and set it into motion (the red button) [Train Station Maintenance]. After the ride is over, make it over onto one of the ledges above and use the shock gloves on the local generator. After the elevator changes positions, approach the wall that can be destroyed and spread the explosive gel here. You will now to have to fight the bandits that assailed Branden and his people.
In here, for the first time (save Anarky and his side mission) you will encounter an enemy with stun gun. Follow the game's instruction and avoid this character's attacks (the red symbols above the head) and do not attempt landing standard, frontal, blows because Batman may then be shocked with electricity. Instead, double-tap the jump key/button to jump over that enemy, only then start landing some blows into the bandit's back.
Note- there is also a good alternative to this strategy, which consists in exposing the enemy to Batman's attacks. You can throw glue grenades, which will stop then and provide you with the opportunity to launch a frontal attack.
When it comes to the remaining enemies, to the extent it is possible, stop them from firing their guns at you. You can, of course, use the disruptor here, and disable everybody's guns. After you have dealt with everybody, approach Branden and listen to the conversation with him, while being prepared to press the key/button to knock the SWAT team leader down. You can now take the ladder and go through the door to the Train Station.
[New character trophy: Branden]
Around, there are four armed enemies and, just like in the case of the situation in the boiler room, it would be good if you could eliminate them without raising the alarm. Unfortunately, there are no vantage points in this area, although if you still want to plan on your actions from below the ceiling, you can use the grapple, extend the rope and pull yourself to it, using the hook.
A good idea to eliminate the enemies patrolling the upper level of this area, is to grab onto the ledge and throw them over the balustrade. What is interesting, if you hurry, you will be able to eliminate in this way, two enemies that are busy with a conversation. The other, recommended, elimination methods are hiding in the venting shafts that are hidden under the train station and using the grapple to pull propane tanks.
After you have secured the area, go North to reach the door to the Control Room. Climb up the stairs and press the button to lower the railway car with hostages and the bomb inside. Return to the main area, make it over to the car's rooftop, using the hook and approach the bomb.
The general premises of the Firefly's second bomb disarmament scene, remain unchanged so, use the Cryptographic Sequencer to play three hacking mini-games that assume time limits (21 seconds for completing the first one, 19 second for the second and 17 for the third). The correct passwords have been presented in the above screenshot.