Over the past few years under Gordon’s leadership, the Organized Crime division has almost eliminated the rise of crime since the Waynes’ death. But Falcone and his partners have become more impatient and desperate. They use Hady, Loeb, and Gordon’s right hand man Bullock more in their operations. However, the good guys made up of Gordon, Grogan, Fox, and Wayne can never prove these city and police officials are dirty.
With these dirty men’s help, Falcone is the top boss in the town and his main competition, yet close ally, The Penguin is second. Falcone decides to makes a bold move. He needs one of his guys to work at or even in Wayne Enterprises so he can bring it down from within. Falcone has one of his friends in the DA office secretly release Joe Chill early. Cobblepot instantly hires Chill and places him into one of his businesses, a cleaning company which he uses for his hotels and other businesses.
Wayne Enterprises uses the same cleaning company so Chill now has access to Wayne Enterprises. Falcone has a contact high up in Wayne Security named Frank Vito. Vito can make Chill a ghost throughout the building and computer system. Chill and anything within a 10 foot circumference of him will not appear on security cameras. His badge will say he is a custodial engineer in case he is approached. His alias will be on file when anyone is looking for that name in the system. Falcone and Boyle want Chill to steal proprietary information that Boyle can use for GothCorp and some of Falcone's fronts which include security and shipping. Chill can access any Wayne Enterprises file from a computer set up for him in a maintenance closet.
Since the Waynes’ deaths, Victor Fries finally has seen his pollution freezing system go from a prototype to being a success in his own home and car. Smaller, private companies who allowed Fries to install his system at no charge have also seen resounding success.
One thing that is holding Fries back from getting more business is that he won’t let anyone that works for him install or service the systems. He has to have control over them. This of course causes more concern for Fox and Wayne, which angers Boyle and Falcone who are already upset that Fries won’t allow others to install his system so they can sell more.
Fries just needs one large private or federal organization to install his system in order for his invention to really take off. Boyle increasingly adds pressure on Fries to add the safeguards Bruce and Fox needs. If Fries can get the public on his side Bruce Wayne would cave in and have Fries’s system in all his buildings.
Wayne Enterprises being the first major private company adopting Fries's system would pave the way for other private major private to follow suit. Falcone and Boyle salivate at the thought of GothCorp to overtaking Wayne Enterprises as the premier cytogenetics company. But why stop there? Falcone wants to push the envelope even further. If Fries has his anti-pollution system in Wayne Enterprises they can use it as a Trojan horse into the computer system so they can slowly bring Wayne Enterprises down. Fries is frustrated that Boyle hasn't adopted Fries's system in GothCorp so why the pressure in forcing Wayne's hand?
Wayne and Fox always back up Thomas's claims and they now have proof that adequate safeguards preventing too much freeze aren’t in place. Inspite of what happened many years ago, they do believe in Fries and don't blame him for the Wayne's death. They offer to partner up with GorthCorp and give more money to Fries so he can hire more staff to help him to focus on the safeguards.
Fries has every intent in keeping safeguards in place but his vigor of putting his system in every public and private building first, then assuring the safeguards are in place has turned off Fox and other savvy businessmen. Falcone continues to put pressure on Boyle to turn Fries and Fries is getting more and more agitated.
Although Fries still feels responsible for the Waynes' death the more he gets pressured to bring down Wayne Enterprises the more he puts blame on Thomas Wayne for Fries’s predictament. If Thomas only listened to Victor, Victor would be working for a Thomas Wayne and both would be very much alive and very much successful.
Boyle, Falcone, and even Cobblepot have lost patience with Victor. Victor won’t work on the safeguards. The crime bosses decide to use Cobblepot’s hotels, other businesses and vehicles as the first prominent organization Fries needs to gain validation. The safeguards won’t be in place yet but if an upstanding businessman like Cobblepot raves about the system, maybe Wayne will cave in. The bosses will make Fries a very rich man but will still take most of his earnings to fund their organizations. They dream of Wayne Enterprises losing more money than it makes and then have the ultimate setup to bring Wayne down. They will burn Wayne Enterprises to the ground and make it look like Bruce did it to collect insurance. Cobblepot will swoop in and take over the property and build a bigger and better Iceberg Casino and Lounge.
Just after Fries installs his system into all of Cobblepot’s buildings, Cobblepot gives the Frieses a free weekend at the Cobblepot Hotel so they could celebrate their 10 year wedding anniversary. In the middle of the night Chill and Killer Croc abduct the Frieses. They are taken through the sewers under the hotel and up to a storage room in the cytogenetics lab deep in the subfloors of Wayne Enterprises. As if the ordeal wasn’t enough for Nora, Jones is wearing his scaly wetsuit and croc mask he always wears when entering the sewers which really freaks her out.
Fries is forced to devote all of his time on making his system to Fox's and Wayne's specifications. This means he must give up on the premise that only he can install and service his systems. His team of assistants now must be giving the go ahead to do everything Fries does. The Frieses are forced to remain in lab 24/7 but Chill can go throughout the building to get Victor whatever he needs. Thanks to Frank DeVito, everything remains undetected by Fox and Wayne. Bruce still has no idea Chill has been released.
Gordon gets wind from his friend, ADA Harvey Dent that Chill has been released and is working with Falcone. Dent doesnt know what exactly Chill is doing for Falcone. Gordon wrestles with the decision to tell Bruce or not. Even though Bruce just turned 30, Gordon wonders if he can handle the news that his parents' murderer is out of prison. Jim recalls the lessons that Bruce's dad taught Bruce. Jim feels soon he will bring Bruce to that fork in the road and Bruce's reaction to Chill be out of prison will define him.
Jim and Alfred meet Lucius in his office. Gordon starts off by saying he feels it's a good time to tell Bruce about Chill and possibly the “inheritance” Thomas left for Bruce that they are safely guarding and preparing for Bruce.
One night Nora and Victor are sick of her being kept in a room full of live diseases and being guarded by a man that swims around in disease infested sewers. Victor and Chill then begin to fight. Vials explode all over Nora and she instantly gets deathly sick. Croc and Chill quickly bring Fries what he needs to stabilize her but they cannot release her to the hospital.
The fight and everything that happened in the lab storage room was a lot for Vito to keep under wraps so the Frieses are moved to GothCorp. Fries still has to work on the safeguards but because he is almost finished he will now devote most of his time in finding a cure for Nora. He cryogenically freezes Nora until he can find a cure. He uses Killer Croc to break in via sewer to every research facility to steal information, chemicals, anything to further Fries's cause. Since Croc's workload has increased, Fries now also has to answer to Croc's boss, the Penguin.
Boyle feels Fries is spending too much time on Nora. Boyle thinks all Fries needs is a few more hours to finish the safeguards. Just as Fries thinks he has the cure, Boyle, confronts Fries. Tension that was building for years between them finally comes to the surface. In an act of rage Boyle destroys everything Fries was working on for his wife. This causes an explosion of spare cryogenic gas canisters used to keep Nora alive to shower Victor. He realizes what has happened to him and instantly wraps his freezing hands around Boyle. Boyle manages to blurt out if Fries kills him Falcone will make sure Fries's last few breaths will be spent watching Nora's body being incinerated. Both men realize they need the other man alive.
Fries loosens his grasp and crawls away heading towards the walk in freezer. Boyle looks at him in disgust and says he wants him out of his building. He will find him a private place where he can still work on Nora's cure, finishing safeguards to his system for Wayne Enterprises and somehow keeping himself alive but he demands the safeguards be done in a week.
The Penguin offers Boyle one of his warehouses by the docs to keep the Frieses and everything Victor needs to work on his system and find a cure for Nora and himself. Chill brings Fries equipment from GothCorp and Wayne Enterprises. Fries develops a suit that keeps his body temperature what it needs to be for him to remain alive. Included with the suit is a 5 ft gun. It is more advanced than the little freeze guns he used on his system to test components to see if they could handle the frigid temperatures. Boyle, Chill, and Croc think it’s just for his research but Freeze made it much more powerful. He also secretly adds flame throwing and ammo shooting capabilities to the gun. When Boyle destroyed all hope for Nora’s cure he also killed everything decent within Victor.
Victor finishes the safeguards but now fully sees the concern Fox, Thomas and Bruce have. But as he thinks of Thomas in particular, Victor gets more enraged. If Thomas only listened to him none of this would have happened. And if Bruce didn’t create such a scene the Waynes would have not left and then be killed. Fries thinks how ironic it is that Chill killed Bruce’s parents and virtually killed Victor’s wife. He will kill Chill when this is over and just as Wayne will be undoubtedly so Fries his gratitude, Fries will take down Wayne Enterprises. Bruce won’t see it coming.
Victors knows he eventually would have won Thomas over, but Bruce ruined that. Falcone, Boyle, Penguin and Loeb never wanted Bruce to die but simply use him as a pawn for their interests. Butscrew them. Bruce must die, just like his parents and maybe even Nora.
Chill killed Bruce’s parents after they left Victor, but the chill from Victor’s gun would kill Bruce. He knew at some point their paths would cross as Victor followed Falcone’s plan but the plan would be derailed when he kills Bruce and Wayne Enterprises.
On a night Chill is not working at Wayne Enterprises, Victor recruits him to go to Wayne Enterprises to analyze Nora’s blood to see if he was making any progress. The equipment Croc stole from him wasn’t advanced enough. It takes a lot of persuading and intimating Chill because Chill isn’t convinced Victor can stay within the guidelines of them not getting caught on camera, but eventually Chill gives in. Freeze develops a tinted visor for his helmet just in case something goes wrong with Vito’s program. At this point Freeze cannot be identified. If the GCPD and public find out he broke into Wayne Enterprises looking like a monster, his bosses will kill Nora.
Right before they leave their hideout, Victor turns to Chill and says, "We are going to make a good team, Chill and Freeze. Isn't that right, Mr Chill?" Chill is relieved Victor now appears to be on thier side. He looks at Victor’s gun and says, "Yes, Mr. Freeze." Victor laughs at his new nickname. "Yes, call me Mr. Freeze from now on Dr. Victor Fries no longer exists."
When they arrive in Wayne Enterprises Chill leads the way and Freeze is able to keep within 10 feet of Chill. But as they are walking in a cytogenetics corridor a video of Thomas Wayne describing how he seeks out the best minds to work in cytogenetics catches Freeze’s attention and he stops dead in his tracks. Chill didn’t realize Freeze stopped until he was at the door of the lab they needed to go into. He realizes Freeze is at least 100 yards away and he sprints to Freeze, yelling at him along the way. Freeze doesn’t hear him because he is angrily staring at Thomas Wayne’s face screaming at him that he is a liar and he will pay for his lies.
Vito was out at one of Falcone’s clubs when his phone alerts him of what just happened at Wayne Enterprises. Chill was not scheduled to be at Wayne Enterprises so there was no need for Vito to work. Vito runs to his car and pulls up his lap top. Vito is not able to completely erase Freeze from the security video on the fly. This crashed the software that made Chill a ghost so he was now visible for the first time. GCPD’s facial recognition software alerts the Organized Crime Division that Chill was in Wayne Enterprises along with a giant robot looking thing. The system instantly finds all the other video of Chill at Wayne Enterprises. This also means that the Frieses and Killer Croc can be placed in the building. Vito verifies that no one at GCPD is currently looking at the video since it is after hours but the on-call officers should be getting alerts to come in to headquarters. All the GCPD and Wayne Security is going by are alerts to their phones. GCPD cruisers close to Wayne Enterprises are alerted and they start to make their way to join the in-house Gotham Security guards who were making their way to Chill. They verify that Chill is in the sublevels at the cryogenics labs. Vito quickly creates a diversion.
Vito instantly destroys all the video and radios into GCPD and Wayne Security that there was an error in the software because he accidently spilled his coffee on the consol. He can’t simply say nothing has happened so he does say that there is what appears to be a disgruntled employee who does look like Chill shooting up the 30th floor. Vito then calls Bullock to give the GCPD specific instructions.
Bullock informs the “good cops” to go to the 29th and 31st floor stairwells. He will go the 30th floor stairwell and try to talk to the employee in case he is holding hostages. Vito then let’s Falcone and Loeb know what is going on. They are furious with Fries and Chill but they have to concentrate on damage control. They conference in Loeb and they all agree to let the media know if anything goes out to the press who then contact GCPD, Loeb will tell them the disgruntled employee story. The public cannot know that Fries has turned into a psychopath or else no one would buy his anti-pollution system and there goes the mob bosses’ cash cow.
Before Vito alerted the guards of the apparent disgruntled employee they were already on their way to the cytogenetics labs because of the first alert they received about Joe Chill. They stop dead in their tracks when they see this robotic looking man in front of them. Some reach for their pistols, some reach for their radios to inform Vito someone is in cytogenetics as originally reported.
For Freeze, time is frozen for a moment as he begins to think of what is about to happen. Chill is about to shoot them but Freeze stops him. He tells Chill, “Your first victims were responsible for making this company the powerhouse it is. You also severely damaged the person trying to protect them. Let my first victims be the ones who are trying to protect his building so I can continue to damage Bruce and his parents’ legacy.” As Freeze pulls the trigger and freezes the guards he sees Thomas Wayne’s face over 15 years ago that night. Freeze knows they still are alive under ice so he hits a button on his to turn into a gun. He asks Chill what caliber did he used on the Waynes. Chill says it was a .40. Freeze selects that caliber for his gun. Ironic how it’s the same caliber Wayne’s own security guards and the same police he helps equip have in their guns. He then pictures Bruce that night and pictures him today and what he hopes his face will be right before Freeze kills him. He then pulls the trigger and blows his victims to smithereens. Chill freaks out a bit. He had no idea Freeze’s gun was programmed for anything besides working on his anti-pollution system.