Assuming that this is a standard action / reaction / counter / etc., the last thing that really kicked Ink's butt is the high mobility and fire power of the Chopper.

This can be countered in several ways.

Armor
Further increase the armor to defeat the bullets. We got a glimps of this with the treeomuth. This mechanism can protect, but lacks offensive measures against the chopper. Trying to get close enough to hold on is more a lottery ticket than a viable stratagem.

Stealth / cover / concealment
Stay hidden. Our heroes have pretty much only shown direct fire weapons. It is much harder to hit what cannot be seen. They have not used anything like mortars. Artillery or carpet bombing. Many of us have speculated that there has been several times where the little ones were "nearby" watching when they were much smaller. Working below ground also exploits this. The Germans of World War 2 called this Rattenkreig when they encountered it at Stalingard. The Russians would use the Sewars and tunnels to suddenly appear and ambush. We have also encountered this several times. However, once the attack is initiated, they still have to deal with ranged weapons. It sure would be nice if Ink had something that could attack while not presenting a part of the body that can result in a lethal wound. Long tentacles like Saul's squid could do this. If a limb is damaged the unit may become combat ineffective, but still able to retreat.

Greater mobility.
Underground, increased burrowing speed. To not just use the existing tunnels, but make new ones. On the surface, think super Jumpers. Jump from building to building like the hulk in the Avengers. Might be able to get to the chopper when it is off the ground. Even better, a flyer. Jumping has the disability that it is not very easy to change direction once initiated. Flying is something that goes deep into the human psyche. A very desirable superpower in humans and evolution. Clams, starfish, crabs, sea cucumbers are stuck on hard surfaces. Fish learned to swim and open up true three dimensional movement. This is so advantageous that it has naturally evolved independently in diverse lineage of animals. Insects, birds, mammals each did it independently.

Increased range
Thrown weapons. A frog's tongue. It allows attacking from cover and surprise. Hell, even throwing a normal biter.

Redundant command / sensory organs
Going all the way back to Chapter one.
Saul: "They are not going down"
Michael: "Aim for the head"

Multiple heads counter this

Later, in season one, Riley gets a bullseye, literally. By Season two, they start trying to cover their eyes while attacking. Increased survivability, but decreased efficiency. Multiple heads is probably a bridge too far, but multiple eyes is doable.

Last, many have noticed similarity to the Bible. One of the beasts has several heads and the body of a lion. The Devil comes in the shape of a dragon and is slain by Michael with a sword.

Michael? Check!
Sword? Check!
Dragon? Stay tuned...

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