Turn east after a short while and jump over a new fence. This is also an area where Killer Croc's appearance is almost certain. Don't forget to use your Batarang before the monster gets too close to Batman. Shortly after that you'll have to make a run for it for the second time. Once you've reached a new corridor turn south and begin moving forward.
Keep moving south and it shouldn't take too long for you to locate the final fifth container (screenshot #1). Use your Batarang and then collect the last sample. You'll now witness a short cut-scene informing you that Batman has activated a beacon which will lead him to the exit. Watch out for Killer Croc, because he'll appear soon after the cut-scene has ended.
Start off by heading north. During your final moments spent in the sewers you should be using your meter to find the correct path. Don't forget that you'll be informed the second you've picked the wrong path. You'll also have to sprint a few times to avoid being killed by the Croc, but it shouldn't be a tough challenge.
Batman will pass by one of the containers along the way, so you'll know that you're on the right track. Don't forget that Killer Croc aside from destroying the wooden planks will also use his previous attacks. Use Batarangs each time to prevent him from getting too close. You'll trigger a checkpoint when you're about 140 meters away from your destination.
Soon after your progress has been saved the camera will change its position, informing you about a new chase sequence. Your primary concern from now on will be to keep running in order to avoid getting caught by the boss. Don't worry about all the gates you'll find along the way, because Batman will automatically get past them.
It shouldn't take too long for you to return to the large tunnel where you've started exploring the sewers. Keep running until you come across a closed gate. QUICKLY choose an explosive gel from your inventory. Wait for the Killer Croc to make his way to the explosives and once he's close enough detonate the charges (screenshot #2) to trigger a new cut-scene.
Once you've returned to the partially flooded corridor make a few steps forward and turn right. Use the Line Launcher and open a nearby door to travel to the Old Sewer. Here you'll want to travel east (screenshot #2).
A large group of enemy thugs is stationed just around the corner. It would be a good to surprise them, especially since one of the prisoners is carrying a firearm. During the fight itself prevent other inmates from picking up his weapon and once you've succeeded proceed towards the second ventilation shaft (screenshot #2).
Make a few steps forward and stop close to a wall. Wait for one of the devices to scan Batman after which you'll be allowed to enter The Batcave. Head forward and don't forget to jump over a small gap. Eventually you'll have to use the stairs again leading to Batman's computer. Watch a cut-scene and notice that you've been equipped with a new toy. It's going to be an Ultra Batclaw (upgraded Batclaw).
The primary functions of your new gadget include grabbing up to three inmates at the same time and ripping off weak sections of the wall. You'll want to test it out immediately on a nearby object (screenshot #1). Once you've created an opening hop inside and use your hook to reach higher platforms.