In the previous part of the walkthrough, you destroyed the Penguin's Jammers. Now its time to go back to the museum to rescue Mister Freeze. The objective should show up now: Rescue Mister freeze from Penguin in the Museum. Now that the jammers are gone, you should be able to use your cryptographic sequencer to get into the museum. Backtrack along the same route you came from, and make your way back up to the surface.
Head back to the museum. Defeat the henchmen guarding the door and re-enter the museum. Now that the Penguin's communication disruptors are out, you can use your cryptographic sequencer on the security console.
Make your way to the museum. There will be some thugs in the Dinosaur room. 3 unarmed hostiles, holding a hostage. defeat the thugs. They will be wearing body armor. Use the Beat Down to take out thugs wearing body armor. Then go talk to the G.C.P.D Police officer who was held hostage, Elvis Jones. HE will tell you that Jim Gordon sent him and that there are more officers in danger.
Your objective now is to rescue remaining undercover GCPD officers in the Museum. Download the GCPD personnel database into your batcomputer. This will put on your map the position of the other officers: Best, Forrester, Strickland, Whitman, Miller, Michaels, Sanches, Denning, Southwold.
Head through the door and onto the hallway. You will find a security override mechanism which is out of reach. Use your remote controlled Batarang to trigger switches that are out of reach. This will open the door . Go through the hallway and you will reach the Gladiator Pit. Penguin will be there to greet you and ask you if you are for him, the cops, or the ice man. You'll answer that you are there for all of them. The Penguin will open the gates and send his goons onto you. There will be lots of them. Fight them all, try to move fast from one to another beating them down. Do not stay in one position for too long or they will gang up on you.
Once you beat them, the Penguin will bring in a Titan Infected Thug. This is a Boss Fight.
Use the Ultra Stun to start a Beat Down on a Titan Infected Thug. Try to stay close to the walls and keep moving. Stun the Thug and beat him. The thug will have company in the form of other goons, but try to focus on the titan thug as he is the most dangerous. Once you knock him down, defeat the other goons.
Alfred will contact you, and you will tell him you found Penguin but haven's located Mister Freeze or the cure yet. The situation is worse then you thought. Penguin has a supply of the Titan Formula. Oracle will join the conversation and wonder how the Penguin got Titan off Arkham Island.