Project LOTUS is the codename given to a biological experiment conducted by SANCTUS. An attempt to create a restorative chemical for combat missions, the project became a biological weapon that killed almost all infected. After SANCTUS went underground, they would continue experimentation on the project and house it in a black site lab. LOTUS became the priority for a criminal cabal called the Pact, whom wished to use its restorative properties.
Years before Batman's operations in Gotham City, SANCTUS, the Agency's scientific division, attempted to create a restorative agent for the human body. Utilizing biological engineering, the group modified an unknown virus and tested it on countless human test subjects, presumably including kidnapped civilians. However, none of the subjects survived, with more tests only killing more. Following the discovery of the experiments, the Agency broke ties to SANCTUS and force them to go underground to survive. Setting up a laboratory underneath the Bohdi Spa, they continued experimentation with LOTUS.
When one the scientists, a former criminal known as "Riddler", was accidentally infected with LOTUS, the scientist quarantined him in the expectation he would die. Instead, Riddler survived, granting him a longer age-span and enhancing his physical condition. However, LOTUS caused severe damage to Riddler's brain chemistry, leading him to develop various psychological problems including Obsessive Compulsion Disorder (OCD) and Narcissism. Riddler was held in the facility to for the purposes of further experimentation and research, but he was able to escape and began plotting revenge on SANCTUS and the Agency for their compliance with LOTUS's experimentation.
To this end, Riddler formed the Pact and recruited various criminals masterminds including Bane, Mr. Freeze, Harley Quinn and the mysterious "John Doe". Knowing they all suffered either physical or mental problems, he informed them of the various capabilities of LOTUS and convinced them to attack SACTUS to retrieve it. Riddler promised to use it to treat Bane's addiction to the steroid Venom, cure Nora Fries's condition, and negate Harleen Quinzel's hereditary mental illness. However, the group were never told about the permanent psychological damage, which Riddler kept secret.
After the Pact arrived in Gotham, Riddler gathered as much data he could about LOTUS and its laboratory. The information would be stored on a supercomputer and a laptop, both of which were linked to SANCTUS's network and encrypted, though could only be accessed safely if a decrypting drive was installed and utilizing Riddler's eyes for the retinal scanner. Riddler kept the supercomputer underneath his lair in the East End, though would place his laptop in the care of Quinzel.
Following Riddler's death, the Pact lost access the information about LOTUS's location. However, they launched an attack on the Agency to retrieve his body to create a safe version of LOTUS for them to use. Unknown to them, Waller and the Agency were also aware of LOTUS and had let them steal Riddler's body to let them access SANCTUS's facility.
Believing Riddler had information in his lair, Harley Quinn sent new recruit Bruce Wayne to recover the data. With the help of John and Selina Kyle/Catwoman, he was able to discover the supercomputer and the decrypting drive. After decrypting the computer, Bruce discovered about LOTUS and SANCTUS, but was unable to access the information before it self-destructed.
Having learnt about the laptop in Quinn's possession, Bruce was able to obtain it with either John or Selina's help. Using retinal goggles created by the latter, he learnt about LOTUS's experimentation, the Agency's involvement and Bohdi Spa. However, the other members were able to learn about it through either Bruce or John informing them. Bane, suspicious of the former, was able to discover the location by following him to the Spa and informed the group.
Now aware of LOTUS's location, the Pact launched their attack on the lab. Depending on who Bruce blamed on the laptop's theft, the following possibilities will happen.
If Bruce blames the theft on Catwoman, he is able to get the LOTUS's laboratory ahead of the Pact. Working on the incubator's controls, he sets it to incinerate the virus samples. When the Pact break into the lab, Freeze works on getting samples before they can be destroyed whilst Bane battles Bruce. After retrieving them, he tries to escape, only to be stopped by Bruce. During the fight, Quinn attacks Freeze, steals a LOTUS vial and locks him within the lab's airlock with several broken ones. With the other samples destroyed, she is able to escape whilst the Agency storm the lab.
If Bruce takes the blame for the theft, the Pact are able to break into the lab without disruption. As they extract samples from the incubator, Batman confronts them, possibly with Catwoman's help. To buy time, the Pact engage the vigilante and battle him long enough for several samples to be extracted. Batman, utilizing either Bane or a sticky bomb, knocks the incubator over, disrupting the samples and forcing it to activate an emergency lockdown. However, Freeze gathers the extracted samples and attempts to escape, but is stopped by Quinn. Stealing one vial, she breaks the others and locks him in the lab's airlock, infecting him with the virus. She then escapes whilst the Agency storm the lab.
With the Agency wishing to continue experimentation on Freeze, they kept him locked up whilst they rounded up surviving SANCTUS employees and equipment to use. During this, Bruce/Batman confronted him on Quinn's location. Freeze informed him about LOTUS's healing properties and Quinn's plans to gain these using Riddler's blood. In return for the information, he asked Bruce/Batman to lower the temperature to help combat the infection. If the offer is declined, Freeze and LOTUS are left for the Agency to experiment on.
During the heist and clean up, Agency Director Amanda Waller sent agents to raid the Pact's lair and gather samples of Riddler's blood. Planning to blackmail them to work for the Agency's supervillain division, they destroyed Riddler's body to ensure they cannot use it to create more samples. However, one of Waller's agents, Iman Avesta, destroys the samples to ensure they cannot.
Keeping the sample with her, Quinn set up plans to hold the Gotham Bridge hostage in return for Riddler's blood samples. During the confrontation, John arrives to either help subdue her or escape, depending on decisions made previously. Regardless of what happens, John gained possession of the LOTUS sample and detonated Quinn's bombs to ensure his escape. John escaped with the virus by diving into the waters beneath, possibly with Quinn at his side.
Depending on whether John becomes a vigilante or criminal, the following possibilities will take place.
If John, now calling himself "the Joker", becomes a vigilante, he keeps the LOTUS sample with him, leading the Agency to send various searches for him. When he finally meets with Bruce, Waller demands that they hand both him and the virus sample, threating to reveal his role as Batman publicly. Joker begins sharing plans to kill her by infecting her with the sample. However, Bruce and Alfred are able to convince not to, but to destroy the sample instead. Using a compartment in the Batmobile, they are able to destroy the sample, ensuring that Waller cannot get her hands on it.
If John, now calling himself "the Joker", becomes a villain, he and Harley begin mass producing LOTUS within ACE Chemicals plant. Making plans to use them to terrorize Gotham and torture Bruce, they create time releasing bombs and scatter them throughout Gotham. Quinn plans on using them to find a survivor and make a usable version of LOTUS to cure her condition.
Releasing the first of these in Wayne Enterprises, they detonate various LOTUS bombs throughout the city, including the Gotham Bridge, the City Docks and Mercy Street Hospital. Using clues from cloth left behind by Joker, Batman is able to locate on of the bombs in Divinity Church and deactivate it before detonation. Joker also approaches Commissioner Gordon and offers the locations in return for Batman. Going though with the deal, emergency services are able to find the bombs before they can detonate.
Joker and Harley also use one of these in their dinner party for Bruce and his allies, planning to use it to execute them. However, after turning them against each other, Bruce is able to disable the bomb and prevent Quinn from detonating it. It is unknown what happens to LOTUS and its dispensers, but the Agency are able to gain possession of it. It is presumed that they would continue experimentation with the virus, much like SANCTUS did prior.
Project LOTUS's effects could vary, depending on the person used on and the strength of the dosage. In most instances, the victim would bleed furiously before succumbing to the virus and dying. However, there was only one known survivor, the Riddler. According to Victor Fries, LOTUS was capable of healing most medical and psychological problems, depending on whether the victim survived. It seems these included addictions to substances and seemingly incurable diseases. However, as Alfred Pennyworth pointed out, it would, in return, cause severe damage to the chemicals in the brain, resulting in permanent damage and driving the person insane.