(Capcom's primary storyline)
Some time after the Annabelle washed ashore in the bayou, the Mold that infested the vessel began to leak out and contaminate the surrounding area and shoreline. Local wildlife soon after came into contact with the Mold, namely, Alligators.
While Joe was bringing back a small dosage of the cure for Zoe to his cabin, several very large mutated Gators lay before him, presumably slain by a rampant Jack Baker as the cabin is engulfed in flames. While Joe was searching for a full dosage of the cure, he encountered more Gators in the flooded swampland.
There is currently a quarantine wall set in place to contain the spread of the Mold. With the Mold outbreak secured within, the Gators continue to thrive.
As the Mold began to fester the swamp ecosystem, alligators soon fell victim to infection. Mutating to abnormal sizes with large teeth that jutted out at unnatural angles, cataract eyes and developing tumorous growths large enough to split open the Gator's tough scale hide.
Gators behaved relatively similar to normal alligators, albeit more vicious. This also changed their attack behaviors, preferring to bite vigorously into prey until death as opposed to drowning them beneath the waters or engaging in a death roll, a signature move of crocodilians.
Gators are capable of performing two attacks: One attack they can perform is to bite Joe's torso viciously, causing him to instantly get killed. The other attack has them jumping out of the water to hit Joe which will usually kill him on "Joe Must Die" They typically use this second move to knock Joe off of ladders to keep him from escaping. When this happens, Joe will generally survive with one point of health left. Any other time this attack is used on "Joe Must Die" however, it is always fatal.
Gators are extremely weak to spears, one throw can instantly take one down on Normal Difficulty. On Joe Must Die difficulty, you need to aim for the gator's mouth to kill it instantly. If a gator is moving towards Joe and he gets out of water, the gator will despawn but spawn at the same location again (the 1st one in normal difficulty and also the 1st one in Joe must Die Difficulty at the beginning of the Quarantine Area are exceptions) if Joe proceeds to the same water area again. This tactic might be useful for those that are aiming to get the "The Only Guns You Need" achievement since it prevents Joe from using his spears.
In VR mode, it is possible to punch Alligators while Joe is on land by moving the VR head set towards them which also moves Joe's range of attack without him leaving the safety of a platform or piece of land. It also is possible to kill Alligators with the AMG-78a and the AMG-Dual. However, only the AMG-Dual is particularly safe because of its ability to charge both gauntlets at once for a better radius. On normal difficulty, the AMG-Dual's double charge attack is a guranteed one hit kill on any Alligator.