If you don't do anything at the game's title screen, you'll get the Statue of Liberty telling Superman that Metropolis will become the base for the evil General Zod before telling him that he is the reporter Clark Kent and that he will fight for truth and justice.
Level One
When you start the game, you'll be at the Daily Planet as Clark Kent. You'll have gauges for your super power (health) and item power (abilities) at the top, with the X-Ray vision being usable at the start of the game. Pressing Start lets you select your power. You can jump really high with Up, and you can also punch and talk to people with A. Punching while in mid-air can help you keep your jump low when you face enemies and jump over their projectiles.
The bald guy to the right is the copy chief, and he tells you to go out and get some news as there is a deadline. To the right of him is Lois Lane, who well tell you that strange things are happening in Metro Park and that you can access the map with the Select button to see where it is. The shield icon indicates where you are. You can only use the map while outside; you cannot use it inside of a building or a sewer. Orange dots are landmarks, while black dots are regular locations.
The guy to the left is Jimmy Olsen, who just takes a picture of you.
Head all the way to the left and go through the door with Down on the D-Pad, then head right and press Down in front of the phone to enter it and become Superman. As Superman, you can move faster and you can also use your superpowers.
By beating up enemies, you can get blue crystals that restore your health. There are also red and green ones, but those decrease your health and should not be picked up. If your health gets too low, you'll change back to Clark Kent. You'll have to refill your health with blue crystals to become Superman again...so watch out for those bullets!
You'll need to beat up enemies to get power-ups. The Roman numerals I and II are Super Breath I and Super Breath II, respectively, and the first one lets you extinguish fires while the second one lets you freeze enemies solid. By picking these symbols up, you can refill the energy gauges for these powers. The eye icon is the X-Ray Vision, which allows you to see ghosts. The Up Arrow icon is Super Flight, which allows you to fly and acts as the fast travel of the game. The Down Arrow icon is Super Spin, which lets you drill into the ground in specific areas. Finally, the V icon is the heat vision, which lets you shoot heat lasers out of your eyes to do damage, especially to bosses. You can refill some of these powers by fighting enemies as Superman in public, but if you want to refill Super Flight, you'll need to fight enemies in buildings.
Pressing Start will allow to switch abilities with the D-Pad. It should be mentioned that you have an attack power and defense power rating on the left side of the screen, as well as Super Hearing, which is a passive ability and is always on. The attack and defense ratings will go up as you progress through the game.
Pressing Select brings up the map, and the flashing diamond indicates your current location. Any yellow dots near where you are indicate where you can use your Super Flight to teleport to, assuming you have the energy to do so, and you can move the white triangle under them to switch where you can go to with the A Button.
You won't be able to enter the subway with Down unless you have a pass.
By going up to signs near doors and pressing A, you can see what that location is.
At the Government Tower, which is just to the right of the Daily Planet and the nearby phone booth and subway, stand near the left side of the doorway, equip Super Flight, then hold Up and press B. This will let you fly to the top of the building. Fight off all of the enemies here, and you'll be told that their boss is at Apollo Theater in Metropolis Park, which is where you need to go next. You'll also get an extension for Super Breath II, which allows you to use it more. To get back to the streets, just leap off the side of the building.
Believe it or not, you're also supposed to go into the building and fight the enemies there for another Super Breath II extension. When you get the extension, the last enemy that you beat will tell Zaora that they failed her. (More on that later.) Because I didn't find this out, I miss out on this one, and I'm unable to get it later in the game as it's only available in the game's first level.
From here, head to the right until you see a building with the word "Help" coming out of the doorway. This is Jewels by Alexander. Go inside with Down and fight the enemies here to get another Super Breath II extension. With the enemies gone, NPC's will line the area, thanking you.
The vertical lines with the small horizontal lines in them are the subway paths. You can use the subway paths in these locations, but you need the Subway Pass first, and you won't get that for a little while.
From here, I don't know how to refill Super Flight manually, so I decide to do it the other way, which is losing all of my health and getting teleported back to the Daily Planet when you continue as well as using a password that I get from the Daily Planet when I head back over there. If you talk to your boss at the Daily Planet when you return there, you'll get a password. You'll also get something that sounds like gospel music playing in the background. As it turns out, the song in question is a Christian hymn called
"Stand Up, Stand Up for Jesus."
From the Daily Planet, I fly to Mt. Royal. To do that, I equip Super Flight, use the ability, press A until I have the white triangle under Mt. Royal, then press Start. From there, I head to the right to Nordham University and use the X-Ray Vision to see the ghosts in the area. The ghosts will try to leap over us, but I can stay on the ground and hit them as soon as they get back on the ground. By beating up all the ghosts here, I can get an extension for the Heat Vision. You don't need to defeat these ghosts for a while, but you'll need to eventually, and I'll mention when.
From here, head to the left until you reach Glernmorgan Square. Go inside and use your X-Ray Vision to see the cat ghosts, and punch them in the face while avoiding their fireballs, which they shoot straight forwards. Beat them all to get a Super Spin extension.