Wait a second. Dr. Berry helps the animals escape because they're about to be "decommissioned", right? But, as we see at the end, they don't need to actually put the animals down to do that. They could easily just remove all of the armor, weapons, and implants, turning them back into a normal dog, cat, and bunny rabbit. I mean, if the animals themselves can do half of it and a homeless guy can finish the job, certainly the people who created them could have done the same. So why didn't they?
They didn't know they could. Dr. Trendle is pretty clearly shocked at the end to see 1 and 2 doing just fine without their suits or medication. In fact, that's probably at least part of the reason why he starts crying when he does.
Bad news. Every year, in Real Life, vice units bust dog-fighting rings and have to put the dogs down. Not because they're "irredeemably vicious" - although a few are. They're killed, by the thousands, because the cost of screening out the crazy ones and then housing, healing, rehabilitating and finding homes for the redeemable majority is almost always more than local animal control agencies could possibly afford. (The Michal Vick dogfighting case was virtually the only exception.) But let's return to the comparatively nicer world of We3: if it's a choice between "decommission, dismantle and remove mental conditioning" for several thousand dollars, or "poison them as they sleep" with twenty cents' worth of bleach, the accounting department is going to insist on the cheaper option.
Why would the government have to steal pets from children to turn into experimental animals. Wouldn't it have been better to breed or buy their own?! Or were the tears of children needed to power the suits?
If it was possible to free the pets from the suits, why didn't the military (or the doctor) just do that from the start?
Well, to be fair, the doctor didn't do it because she knew the that the animals were all going to be terminated; she had enough on her conscience already, and she had zero intention of helping the government carry it out.
I have no idea why people think the covers mean the government project kidnapped those pets. Lost pets do get in animal shelters, and the simplest explanation was that they obtained the pets from some animal shelter before the owners got there.
Having members of three different species communicate, let alone cooperate is a bit far-fetched even by comic standards. I mean, some of them (2 and 3 to be certain) even do not have concepts for "friend" and "foe" in their psyche as we understand it - only "food", "danger" and so on. But they clearly need to follow some sort of rules of engagement to function as a team, so they actually have to have a conscience of a human (or something closely resembling it, like a dolphin) to do all this stuff - only they cannot communicate their thoughts properly.
Part of it is probably some creative brain surgery and/or drugs and large amounts of behavioral training, but mostly they seem to be able to work as a team because 1 is smarter and bigger than 2 or 3 and can boss them around, and he's a dog - pack animal to the bone. He's the one who reacts immediately and decisively whenever the other two are threatened, too; I think we only see 2 back up 1 on one occasion, and that might just have been 2 taking advantage of 1 being threatened to flank their enemy. And they do seem to all have the concept "We3" hammered into them on the same level as kill, eat, shit and sleep, even if 2 and 3 have a more limited understanding of it.
I do not see how the gear they are wearing could be removable. Its control systems have to be hardwired to the animals' central nervous system to function, for one thing, and I doubt it is done through a handy plug socket. Considering the subjects are non-human, and, in the end, expendable, the process of cyborgisation is likely to be non-reversible. Certainly not by themselves and some random guy. So the ending may be considered a compromise between realism and the author's wish not to have a completely pitch-black and hopeless closure.
And even if the suits are removable, how did 1 and 2 get them off? It's not like one of those doggie sweaters you can wiggle your head out of if you try hard enough; they'd need thumbs to manipulate the suits in that fashion.
Considering how much dogs and cats hate to wear clothes, the real miracle is that they kept the titanium plating on in the first place.
In the opening, we see the animals' suits include shields to protect their faces and hide what they are, but after they return to base, those are never used again. Are the animals unable to put those shields down themselves? It leaves their heads extremely vulnerable. Likewise, why was 4 deployed without a face-covering mask? It might've kept him safe when 2 clawed out his eyes.
I may be misremembering, but it seemed as if 4 was rushed into the field. Facial armor seems like an odd thing to leave until the last moment, but it's possible that 4 didn't take as well as the earlier ones did to having its natural senses blocked off. For that matter, preferring the open air on their faces may explain why 1, 2, and 3 don't deploy the shields themselves: not being armadillos, they don't really grasp what 'armor' does.