This tip is the part 11 of the mission underground retreat walkthrough featuring a weakened Superman for helping Batman and Robin traverse the subway system and continue to deal with the Joker shaped vehicle.
Citizen in Peril
After the first Checkpoint use Lexs Deconstructor which is on the pile of junk in front of the green boxes down the train tunnel.
Find someone with super strength to pull the Orange Handle for saving the trapped citizen.
Switch to the Penguin to blow up the silver object in the opening area with his minions. Pull the lever to find minikit
Use Lexs Deconstructor to shoot the wall behind the large turbine. Go to back there to pick up the Minikit.
From the last Minikit, stick your way to the lower part of that area to open the Riddler Box there.
Checkpoint Running Subway Cars
Switch to Poison Ivy and use the Flower Bed which is on the other side of the track.
Switch to Batman and don the Sensor Suit.
Pull the lever in the back corner by activating the suit first to open the blue cage next to it.
Then clear out the junk inside and collect the Minikit with Batarangs.
Clean and wash the 7 bits of graffiti off the walls with Aquaman.
Get over two-Face graffiti on the other side of the train with the Flower Bed.
Riddler graffiti which is on the raised platform in the center of the area with the switch that stops the trains.
Joker graffiti which is on the center platform between the green boxes and the electric floor.
Two-Face graffiti which is on the left side of the center platform between the green boxes and the electric floor.
Two-Face graffiti which is on the left wall in the area the giant robot hand deposits you. Get the one with the big fire.
Riddler graffiti in the area with the big fire.
Joker graffiti in the area with the big fire.
Fly up to the walkway on the left side of the train tunnel.
Find a Minikit at the far end.
After rescuing the Citizen in Peril, rip off the door of the train car with Cyborgs magnet power.
After fighting off the giant robot hand, use Lexs Deconstructor on the boxes on the far right of the area to build with the bricks then push the green pad.
Checkpoint On the Train
Remove the blue panel on one of the train cars with Cyborgs magnet power. Drop in and pickup the Minikit.
It is sitting on top of the lead train car. Fly Superman up there to nab it.