Table of Contents
Watcher in the Wings
You will find him first across and to the left (south) of the GCPD building. He will talk to you and leave a symbol on the ground. Scan it.
You will also meet him on top of one of the buildings south of the courthouse. Look out from the courthouse steps and the building across the street to the right. He should be on the corner closest to you.
You can also find him on top of the ferris wheel in the Industrial District. It's in the eastern part of the district, by the water. Climb up and talk to him.
You can also find him Northeast of Catwoman in the Bowery. He will be on the NW corner of the building and he will leave another symbol on the ground. After this, the map will open up and Batman will notice that the symbols line up. The answer to this puzzle is as follows:
You should have 5 circles. There are three very close together and they should be toward the top of the map. Four of the circles will be points where you met the watcher. The top middle circle will be on the right side of the Church, upper left will be south of the courthouse, upper right will be just west of the GCPD, lower left will be just north of the subway entrance in the Bowery and the bottom right will be just north of the east side of the Steel Mill. This will reveal the 5th spot by the church. Go there and then if you look NW then you should see the last symbol on the wall. Scan it.
Note that the Watcher may not appear until you finish the story line for this section. 
Shot in the Dark
There will be a distress beacon from a building in the Amusement Mile. On top of a building Southwest of the GCPD you'll find a political prisoner. Talk to him and he'll be shot. Enter detective mode and scan the point where the bullet struck to trace it back to it's source. Follow the line back into the industrial district and examine the crime scene to find a bullet casing. After this, you will have to wait for Oracle to give you a call and tell you there has been another murder.
This is going to be in the Northeastern part of the Park Row area. East of the courthouse is a broken bridge and the new body is on that bridge. Check around the body again for another bullet hole. Scan that in evidence mode and then follow the trail eastward. On the building that the trail ends, you will find a tripod on the corner closest to the body. Search the tripod for evidence. Once you've done so, you'll have to wait for Oracle again.
The third victim is in the street NW of the words Park Row and SW of the courthouse. You'll actually hear some thugs talking about it and you'll have to take them out before you can check for evidence. Follow the line from the bullet hole over to the wall. There will actually be another hole where the line ends because the shot was ricocheted off of here. Examine that to get a trajectory for a building between the church and courthouse. On the corner closest to the victim, you can see some snow has been melted. Examine that.
On top of the NE substation, one of the three hatches will have a PDA behind it. Hack the PDA to find out Deadshot's location. Then you need to get to his position in three minutes and it's north of the Museum. Once you get there, you'll have to fight Deadshot. Stay crouched and move from cover to cover whenever he turns away. When you are close to him, wait for him to turn away and then rush him and attack him. Just keep striking him and he'll go down. Mission accomplished.
You'll find this on one of the building SW of the Courthouse. It will be marked on your map. This is mostly just a combat mission. When you start fighting, keep the common enemies at bay but focus on attacking the glowing guy (who will remain nameless so as not to spoil). The common enemies will spawn endlessly until you take the main guy out. He will also shoot a lightning attack at you if you don't hit him as soon as he appears. He will then disappear once hit and then reappear again so keep your eyes peeled for him.
Once you've hit him a few times, do a ground takedown on him to finish the Mission
NOTE: This will contain answers to Riddles, you've been warned.
Head to the church and you'll be presented with a Riddle. The answer is Organ so scan the organ at the back of the room. Head to the Court House and back to where Two-Face was. Take out the thugs there and you will be presented with a number puzzle. You must line up the numbers so the bottom number is 275 and the right number is 325.
After this, you'll be given a word puzzle. The answer, is secret. He will then reveal the next location. Head to the building marked and by the street at the bottom of the building you will see a wall with a question mark on it. Examine the wall and you'll punch through it. Go through the door and listen to the Riddler talk. Turn around and on the wall there will be a question mark. Throw a baterang at the dot of the question mark to unlock the next door. In the next room, you can use the line launcher to get to the safe tile across the room or you can throw baterangs at the different question mark switches around the room to reveal a path. Either way, once you get to the other side, use a baterang on the switch to your left (as you look toward the entrance) to raise the platform. Glide down to the hostage and rescue him.
At this point, if you haven't found enough trophies and riddles, you won't find out the next hostage location. Keep finding statues and solving riddles until you are informed that you can use the Enigma Machine. Open it and the solution to the riddle is "darkness."
Head toward the way point and check the back of the building for another false wall. It will have a question mark on it. Walk up to it and inspect it to break through. Inside, jump down onto the button to start a shell game. Don't bother keeping track of the shells. Flip on detective mode to see where he actually ends up. The second hostage will be under the left shell . Time to collect more secrets.
You will receive a transmission of a distress beacon near the GCPD. The flare is just south of the GCPD. Head up to the roof, take out the group on the helipad and then head inside to talk. Your mission is to take out the six Titan tanks around the city. They will all be marked on your map.
Industrial District - This container is west of the Steel Mill and it might be guarded by a few enemies, possibly armored. However it shouldn't pose any serious challenge.
Steel Mill - It's just inside the back door. Do the mini-stalker sequence outside and then walk in, turn left and it should be there.
Wonder Tower Foundation - This is the area with the big predator area that has the elevator shaft in the middle and leads to Wonder Tower. In this room, on one of the sides (east I believe) is the Titan Tank waiting for you to clear the room. Of course you could also skip clearing the room, blow it up and leave too.
Subway Tunnels - This tank is by the exit that leads to the Subway Terminal and is just beside the wall mural of Solomon Grundy.
Bowery - Just outside of the Subway, head east and then take a right (it will appear that you're in the southern section of the Subway Station but you are above it) and the Titan tank should be right there.
Museum - Go into the museum and head for the War Room. The Titan tank is in the Southwest corner of the room but you have to go around the right side and come behind the gate to get to it.
After you've found all of these, head back and talk to Bane. You'll be interrupted by a bunch of goons. Take them out but watch out for where Bane is because he can hit you if you jump in his way. Once the Thugs are out of the way, destroy the six remaining tanks of Titan. Mission complete.
You start this mission just southwest of wonder tower. You'll see a dead body on the ground level. Examine the body and then examine the blood next to it. Follow the blood trail around the back of this building and talk to the prisoner there.
The second victim is just Southeast of the courthouse. Head to the group of buildings there and you'll notice an alley in the middle of them on the north side (visible on the map). Drop down into the Alley to find the victim. Examine the body and then the knife on the ground nearby.
The third victim is in the alley just south of the Ace Chemical building. He will be down in middle of the street. Examine the body and then the bleach by his foot. Follow the trail of bleach to the alley just West of the words "Park Row" on the map. Interrogate the guy there and you'll get a waypoint for just Northeast of the courthouse.
The place you're looking for is a little hard to find. Drop down into the alley that is marked. Look into the alley from Catwoman's apartment, drop down and take a left to the end of the alley. There will be a door that you can go through here. Go into the house and then on the table, you will find a personal journal. Listen to it. To get out of the trap, there is a panel over by the crib. Hack it to open the gate and head out. Mission complete.
The building that has Nora is in the NW part of the blue circle on the map, just to the east of the bridge that leads to the Industrial District. It is also the same building as where you can switch to Catwoman. From the bridge, throw a freeze grenade into the water for a raft and you should see an anchor you can use to draw you closer to the destructible wall. Blow the wall and pull the raft into the building. Hop up onto the ledge and go through the door there.
Climb into the vent and into the next room. This is the only other room in the building and it's a fight. There are ten enemies in here, two have armor, two have shields, and two have knives. There are also plenty of things to be thrown and two weapon chests. In this fight, you need to be very aggressive with your takedowns and baterangs. Make sure you keep moving and once you've cleared the room, check out Nora. You'll be told to return to Mr. Freeze in the GCPD. Do so to complete the mission.
You start this mission at the GCPD but you don't actually do anything until you receive your first call at the Museum. The first call will give you a minute to reach the northern part of the city
Monarch Theater - This phone will bring you just north of the Steel Mill by two buildings. Just keep this in mind when navigating so you don't bump into the restricted area.
Industrial District - Head north from the front gate of the Sionis Steel Mill. The phone should be in the vicinity of the ferris wheel. This phone will take you to in front of the GCPD building.
GCPD - Later, you will be able to receive a call here. This will lead you all the way across town to the Museum
Park Row - East of the Courthouse under the bridge. This phone will lead you to the Northeastern part of the Industrial District, east of the Catwoman building.
Amusement Mile - If you walk out of the GCPD and follow the street in front of it to the T-intersection, there should be a phone by the building direclty in front of you. This phone will take you west of the courthouse.
Park Row - West of where it says Park Row and north of where it says Bowery on the map, at the corner of the two streets. Goes to SE corner of the Catwoman building in the Bowery.
Bowery - The Southeastern most point of the Bowery, butting right up against the Restricted zone. This will take you to NW of the Steel Mill.
Once you've done all these, you will find Zsasz North of the Steel Mill and just south of the bridge. Once inside the building, walk towards the next door and turn right to see a vent high up on the wall. Use the batclaw to pull it down, grapple up and climb through the vents.
Once you reach the other side, follow the simple path until you come to a few pipes that you can slide under but don't. Wait for the water level to rise, throw an Freeze Blast onto the other side, then slide through. Wait for the water to go down and grapple up to the other side. Jump over the saw and then make a raft here and use the anchor points to pull you over. Climb up the other side and walk up behind Zsasz. Do a takedown through the glass.
See the next section for details.
This mission is actually quite easy. Go to the Northeastern side of the museum and you'll find a door. You'll have to take out a couple of enemies but once you do, approach the door to be let inside. Talk to the cop inside and he'll give you an upgrade for the Disruptor that allows you to change mines to trigger when guards walk by or to set them off. And once you have the upgrade, the mission is over.
Hot and Cold
You receive this mission from Harley Quinn on your return to the Steel Mill. She'll be tied up in the Assembly Line area. Talk to her for this mission.
Travel to the Steel Mill and make your way over to the Loading Bay how you like. In the loading bay, you want to open the shutter door heading east. Open the door and in the next room you should come to a couple of elevator shafts. Use your sequencer to hack the panel and open the doors. Stand above the left elevator and raise it (you can clear the enemies if you like) then head into the right shaft while the left elevator is raised and hop down under the left elevator. Grapple up to the ledge from there and take out the two enemies. Head into the next room.
In the next room is actually a rather messy group of enemies. Even though this isn't a stalker section, if you can I would deactivate two of the three guns in the room and then freeze the armored guy. This makes the fight much easier. Just head for the one active gun in the room and take him out. Now you're just left with a mostly normal group. Just use a takedown on the armored guy once he's free and you'll make quick work of this group.
Head to the next part of the room and you should see the box with the new gadget to your left (it will glow gold in detective mode). This ends the mission.
Acts of Violence
For this mission, you actually just have to save Politcal Prisoners scattered around the city who are being attacked. You'll hear them yelling for help and a little marker should appear on the map as long as you're nearby. This is actually pretty simple for the most part. Just make sure you save them as you find them so you don't have to find them again later. I don't believe there are a set number of these so just keep wandering and you'll find them. And when you go to save someone, it's usually just a single enemy who will be holding the guy against a wall making him very easy to sneak up on. Just watch for random enemy spawns nearby.
The first training involves simply gliding through the 5 rings. Just run off and glide and turn left and right as needed.
This level requires you to dive bomb. Glide through the first ring and while you are above the second one, hit the RT/R2 to dive bomb strait to the bottom. If you hit one, you should hit the others.
This is a little tricky. Fly over the column of rings and dive bomb but as soon as you hit the bottom most ring, return to a regular glide and continue forward and slightly right to the next ring. Make sure you pull back on the stick so you climb a little bit after you dive bomb. You have to make it through this ring and one more beyond it to finish.
So fly over to the first column and dive bomb but as soon as you're done, pull up and head to the next column. The goal is to be high enough that you can dive bomb through the second set of rings. Do so and then you just have to glide through a couple of rings beyond the column (which will be slightly left of this column).
Advanced Level 1
This seems simple at first but turns into a nightmare. You have to glide off of the sign by hitting A and pull back on the stick so that you make the first ring. Then you have to dive bomb through the next two rings and let off close to the ground to hit the fourth. Getting the fifth is tough. When you let off of the dive bomb, you want to  pull back only about half way on the analog stick so you don't fly into the ground nor fly into the wall above. Then you still have to maintain your flight through the tunnel without crashing. Try going lower than higher because the curved pipes are easy to crash into, even if you think you won't.
This will take a lot of practice to get.
Advanced Level 2
Start gliding towards the first ring and then Dive bomb as soon as you get to it so that you're going through the bottom part of the ring. You actually want to level out a little early and this should help you have control better once you get inside. Hit the second ring, go inside and hang a left. Be careful not to hit walls and there's an island in the middle before the last ring. Don't accidentally land on that.
Advanced Level 3
This is similar to Advanced Level 1. I start at the back of the crane so I have more time to get oriented. Jump off from the back and approach the first ring. Dive bomb through the first ring and when you're about half way to the water, let go of the dive bomb and correct yourself. Then just coast through the tunnel. The only thing that's tougher about this one is that if you fail, you are let off in a group of thugs so you need to pay attention.
Advanced Level 4
For this, you need to glide forward, dive bomb and do a 180 at the same time, level out and coast backwards. How you actually do this is that you want to glide towards the first ring but start turning left just before you Dive Bomb. You want to stop pushing left when you are about half way through your turn and then quickly pull back on the stick and stop the dive bomb. If you manage to get under the bridge then you're golden.
Grapnel - you will use this to get around. You can aim where you want it or just hit the RB/R1 button to fire and it will pull you up to the nearest vantage point. Once you get the upgrade by doing the augmented reality training, you can use it to slingshot yourself over a building by double tapping and holding the A/X button while be pulled up. It does take a decent distance for the boost to kick in for that but you can use it to keep you gliding across the entire city.
Baterang - the Baterang is one of the most used tools aside from the grapnel. You can use it to hit switches, stun enemies in combat, and it's useful for taking down to enemies at once. Just throw it at one target and glide kick the other and then they are just a couple of ground takedowns away from being out of the fight.
Remote Control Baterang - this is exactly what it sounds like. You throw it and then control where it goes. It takes a little effort to control and the controls are inverted from the start. Keep in mind that it can speed up, slow down, or do a U-turn by a simple button press. It's not overly useful in combat and only needs to be used a few times throughout the story so if you don't master it, don't worry about it. Of more importance is its use as a reverse baterang. Hold RB/R1 instead of hitting RT/R2 to activate the Reverse Baterang.
Reverse Baterang - while at first it may seem like a useless tool, it can be used to great effect redirecting someone's attention. It's not great for combat because it requires time to lock on to its target but it can be very useful during predator sections. It can often redirect an entire group of people, allowing you to quickly sneak up for a silent takedown on one. Keep in mind that the guards will be on alert after this and will probably be jittery which means they'll occasionally look over their shoulder quickly to see if you're there so if you go for a silent takedown, be quick.
Sonic Baterang - The sonic baterang isn't particularly useful in combat (in fact, it doesn't have a shortcut) but it can be quite useful for predator missions. It's first use is that it can draw attention by making a sound. This will draw the nearest enemy over to it allowing you to deal with him as you please. It will also disrupt heart monitors making a target appear dead. Lastly, when you upgrade this gadget, you can add an explosive to it so that you can take out an enemy who gets near it. The only down side to that is the explosion disrupts the use of any future sonic baterang.
Batclaw - this has some good combat usage. It can tug an enemy or pull a weapon from their hands during combat. Otherwise, it is used for rafting to move around, to open certain mounted objects on walls, to grab distant Riddler statues or to break certain wall objects.
Remote Electrical Charge - This gadget is used to activate a variety of electical devices from shutters to magnets. Hit one shoot button to flip the device one way (for instance, pull on a magnet) or hit the other shoot button to do the opposite (in this case, push). It is also a useful device for combat. If you shoot it at an enemy, it will stun them and if you shoot it at one of the one armed enemies, it will cause them to spasm and swing their weapon in a circle damaging any enemies nearby.
Disruptor - In the story, this is used to deactivate Mr. Freeze's weapons. When you upgrade it, you can use it to deactivate enemy guns which can make a difficult fight easy. It does take time to activate for each use and after you've used it twice, there will be a long recharge before you can use it again so this is definitely best used before a fight rather than during one.
Freeze Blast - this can be used during combat to freeze an enemy in place and they will remain frozen until you or somebody else breaks them out. It can also be used as a mine during predator sections and when thrown into water, it will form an ice raft that is used to navigate certain sections. This is a great way to take a dangerous enemy out of a fight early. It's use as a mine requires you to upgrade it first.
Freeze Cluster Grenade - Slightly different in effect from Freeze Blast, this gadget deploys a cluster of freeze bombs that can freeze the legs of multiple enemies. While it freezes multiple enemies, it only does so to their legs leaving them with the ability to attack you. What this means is that the Freeze Blast is far more effective on an enemy with a gun while this is more effective on a group of melee enemies.
Explosive Gel - Explosive gel is used primarily to destroy walls and things to gain entry but it can also be used to hit buttons or in combat. In combat, you can use the Quick Gel shortcut to drop some on the floor and then hit it again to trigger it. The neat thing about this is that a little marker will appear on the left side of the screen informing you of how many enemies are on the gel. You can also use it in the same fashion for Predator or you can also use it to shoot a section of wall or ceiling at them by placing it on the far side of the barrier.
Line Launcher - this tool is sort of a horizontal grapnel. Primarily it's used to cross gaps in an enclosed space. You can upgrade it twice. The first upgrade allows you to shoot it again while using it, allowing you to move in a 90 degree angle from where you were headed. The second upgrade allows you to stop on the line and tightrope walk on top of it. This tool will be used far more for solving Riddles and finding trophies than almost anything else.
Smoke Pellets - The smoke pellets primary use is to distract gun men. It can also be used in regular combat to confuse any number of enemies. On melee enemies, it might allow you to take out a couple before the smoke clears. However, you'll hardly find yourself needing to use it on melee enemies. If an enemy with a gun starts shooting at you, the game will even prompt you to use them. Do so and you can likely take out your attacker and/or very easily escape from the area.
Cryptographic Sequencer - This is used for only two things. The first time you will use it is to hack into different radio frequencies by lining up a couple of lines on a specific point or set of coordinates. This is largely used during the riddler challenges. The second time you use it will be to hack a panel. You will find panels all over Arkham City. Some will require special encryption codes that you only get as you progress through the city. Once a panel is hacked it will trigger something like a door to open or a lift to move. This is used extensively throughout the game, particularly in finding riddler trophies. It has two upgrades, one that makes hacking panels easier and another that increases the range so you can hack the devices from further away.
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These people provided additional information that I was lacking in my guide. Thanks for the help, it saved me a lot of time.
 love_hate_111  JWard  Scrinnameless  Smokey Rules
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