Swing through this section of the tunnel until you find some infected and sentries that are fighting. You can defeat the enemies on the bottom floor if you like but it's not required. Make your way to the upper level and take out the enemies there. Remember, where there are infected, there are lots of throwable objects.
On the top level will be a tunnel with a lot of acid. When you go through, a door will close behind you and you'll have to fight some infected. There should be about three of them and there's a couple of throwable items in here. Once they are defeated, find the small crawlspace on the wall nearby. This will take you through to a giant tank. Turn right and in the corner will be a Magazine.
There's a giant valve right in front of the tank. Turn it and then head far to the left. Along the outside of the tank on the left side will be a red pipe that leads downward. At the bottom, web up the fan and go through. There are three valves in this room. About halfway to the top, you will see a platform in the middle with a giant pipe. Attached to this pipe is one valve. You need to stand on this platform just behind the acid to pull on it.
Pull that valve and then hop down to the left side. On the bottom floor along the left wall will be a Magazine. Head as high up as you can on this side. You should see a fan right next to the tank. Jam it up and go through. On this side of the fan is another valve you can pull. You'll need to Web Rush onto the yellow and blue boxes in the corner of the room to pull it. Go through the fan again and down to the bottom floor. Follow the outside wall until you come to one last fan on the bottom floor. Jam the fan and then while still standing on this side, pull the valve.
Head back up to the recently opened door to head inside.
Piranha
You'll find yourself standing in a pool of water and being attacked by a giant Piranha cross-species. Find the valves along the outside of the wall and pull one to lower the water level. Now fight him like you did with Vermin or Scorpion.
After you've dealt a significant amount of damage, he'll summon some minions. Unfortunately, they all are similar to boss creatures except a little weaker. What this means is that you will not stun any of them. If the room has water, remember to lower it with the valves. If you start running out of health, Web Rush around the room until you've healed.
Fight off the extras and then start again with the main enemy. You should take him out before he summons any more help this time.
*Achievement: Deeply Sorry
A door will open here. Go into the tunnels and find the crawlspace ahead. Head through that and you'll come to another two level room with infected and sentries. Again, you don't actually have to fight these enemies but it'll likely make it easier. Whichever path you take, head to the upper level and find the hallway with the half-wall. Go over it and then go through the acid covered tunnel with Web Rush.
On the other side, make your way up using the red pipes to move safely along. At the top, you'll find another crawl space. Go through it and you'll come to a room with a single infected. The infected will be looking through a broken grate. Go through the gate.
Lizard, Round 1
Gwen will be standing on the Hunter in the middle. A group of infected will swarm her on the bottom and a few of the heavies will stand on the platforms above spitting at her. Go around and get rid of the spitters first and then head down to the lower level. There's a ton of things to throw in this room so don't be shy. I'm not sure you could really use all of it even if you tried.
Take down the group in the middle and once all the infected are down, the Lizard will appear and grab Gwen. When he does, use Web Strike to knock him off. He'll run off.
After he does, more infected will appear the same as before. Again, start with the spitters, take them out and then head to the bottom for clean up. Once they are down, the Lizard will appear again and you'll have to Web Rush him again. Repeat this entire process to finish this round. Hop on the Hunter to chase after the Lizard.
Lizard, Round 2
In this round, you'll have to fight the Lizard until you trap him and while he's trapped, you need to head to the hunter and search it for the serum. Fight with him and deal damage until he makes his way over to a spot near a wall or the train. When he does, hit him with a Web Rush to trap him. Once he's trapped, Web Rush to the Hunter and start hammering the Strike button. The Lizard will free himself and attack you so be ready to dodge. Repeat this process until you get the serum. If you're fast with your button presses, you should be able to get it in two tries.
Lizard, Round 3
You'll find yourself in the sewers, crawling through the water. Just keep walking forward until you get out of the tunnel and into an arena shaped room. The Lizard will try to attack you but then move to the outer ring. He'll hop from platform to platform out here. When he is, hit him with the Web Shooters to slow him down. Once he's well webbed, hit him with a Web Strike.
You'll be brought up to him and start attacking. Keep hitting him until you are prompted to dodge. Dodge a few times and then keep hitting him. You'll knock him over the edge and then have to try to stick him with the serum. Keep hitting the strike button. You likely won't get him this time. He'll knock you off and you'll be falling. Use Web Rush to get back up to the central platform. When you land, he'll start wandering around the outside again so hit him with the Web Shooters. When he's stuck again, use your Web Rush to hit him again. Go through the combat motions again and then you'll have to try and stick him with the serum again. This time, hopefully, you should succeed and... WIN!
*Achievement: Welcome Back, Friend
And depending on your difficulty, you may get any or all of the following:
*Achievement: Peter Parker
*Achievement: Vigilante
*Achievement: Spider-Man