I have a theory about how the war ended. I mean, come on! As far as we can tell, the Animorphs only won the conflict on Earth. A lot of Yeerk forces may have been deployed there near the war's end, but not all of them. It's also strongly implied that there was only one Pool ship and one Blade ship in orbit at the war's end. There is conclusive evidence to show that there were numerous makes of these models and they were probably scattered at different strategic points across the galaxy. It's also been said in the series that the two major planets that the Yeerks had under their control were the Taxxon and the Hork-Bajir homeworlds, with a small collection of other, unimportant worlds and outposts. That's not a lot, even if we take into account the very possible fact that the Yeerks were probably in the process of secretly taking over other worlds that the Andalites did not know about when the war ended.
Here's my theory.
I am of the opinion that once the battle for Earth was won, the Earth liaison forces (mainly the Animorphs) gave the Pool ship to the Andalites to use for special intelligence missions. It was these intelligence missions that really ended the war. Since the Taxxon planet seems to be the more important planet in comparison with the Hork-Bajir planet, considering that there were multiple spaceports across the planet, I firmly believe that the Andalites would have chosen to hit that planet first. It wouldn't have been hard for Andalite spies to find a Taxxon to acquire with the great numbers of them that defected on Earth. Thus, before they all morphed permanently into the forms of gigantic snakes, Andalite spies acquired them, maybe even going so far as to obtain a few Yeerk morphs as well. After all, there were plenty of them within reach once the Yeerks were neutralized on Earth, so again, acquiring them wouldn't have been difficult.
Then, as I see it, the Andalites take their newly acquired Pool ship and load it with highly trained Andalite warriors and spies. They take the Pool ship to the Taxxon homeworld and land in one of the spaceports. It wouldn't have been hard to get in because they basically have access to all of the Yeerks' communications data. Once they are on the ground, morphed Andalites secretly infiltrate the spaceport and disable sensors and security, especially if they were morphing into both Yeerks AND Taxxons to create a real morphed Controller, because it is very probable that there were Gleet BioFilters located at all the entrances and exits of the spaceports like there were around the Yeerk pool. Maybe a few Andalite Controllers disable them along the way too.
I also believe that while they were on the Taxxon homeworld the Andalites would have recruited the Taxxon rebels by offering them the opportunity to morph into another form if they helped them liberate the planet. After all, it was going to happen anyway, and the Taxxons had everything to gain by helping the Andalites, and even though the Andalites could have done it on their own, they still needed all the assistance they could get right now. "The enemy of my enemy is my friend" and all that.
So, secretly and slowly, the Andalites also took over other spaceports across the planet in this fashion, disabling vital systems along the way. They had to complete this before a certain amount of time has passed, though, because in my mind the Andalites would have amassed a large fleet to swoop in and hit the crippled planet once their operatives had been on the surface long enough. Thus, once they have disabled the spaceports, the Andalite fleet pops into orbit and the battle begins. Andalite Controllers and Taxxon rebels rise up against the Yeerks. The Andalites in the Pool ship storm into the spaceport and help their comrades. The first spaceport falls quickly and the Andalites have a starting point to launch strikes at the other spaceports. The Andalites begin landing more troops on the conquered spaceport and within hours, a few days at the most, the Taxxon planet has fallen and the Yeerk threat there has been neutralized.
My theory leads me to believe that at this point, with a Yeerk planet under their control and major access to the Yeerk communications network, the Yeerks would have been split in two as to which direction to take. Some, like the Council of Thirteen, would remain adamant on infesting other species. But growing numbers would argue that there was no real need to move against other species now that they could simply morph into nothlits and assume other forms. But the Council of Thirteen doesn't listen and disillusioned Yeerks flock to join the burgeoning Yeerk Peace Movement. (Some may argue that the Peace Movement was limited only to Earth, but I think that there were at least a few members and supporters on other planets.) Within a few weeks, the Yeerk Peace Movement has enough members now to begin staging guerrilla strikes against the Yeerk forces, all the while the Andalites are building up their forces in preparation for an attack on the Hork-Bajir homeworld. The Yeerk Peace Movement contacts the Andalites and promise to help them liberate the Hork-Bajir homeworld if they will let them morph into nothlits. The Andalites agree.
Like the Taxxon homeworld, the Hork-Bajir homeworld contains resisting Hork-Bajir and the Andalites can easily send in some of the ships they captured on Earth and the Taxxon planet, insert a team of morphed Andalites, slowly weaken the planet's defenses, and wait for reinforcements to show up. I think the Hork-Bajir planet would have fallen in this way, with the Andalites landing, making contact with the rebel Hork-Bajir (who are smarter than the average Hork-Bajir since they were created with the sole purpose of fighting the Yeerks in mind) and the Yeerk Peace Movement members, and then causing as much trouble as they can until the fleet arrives.
Thus, the Andalites have taken over both of the major planets that the Yeerks possess within the space of a few short months. At this point, the Yeerks would have realized that they were not going to win the war and opened peace talks with the Andalites. The Andalites offer to let them morph into nothlits and live different lives if they quit the fighting, and the Yeerk vissers surrender. I imagine not ALL of them would give up, and there would undoubtedly be a few isolated pockets of resistance over the next several months and years, but by then, the majority of Yeerk forces would have morphed, and those that neither surrendered nor morphed have been pushed back to the Yeerk homeworld and returned to their pools, where the Andalites now concentrate the bulk of their fleet to prevent the Yeerks from rising up again.
Good theory? Whoa, after writing this, I'm beginning to want to actually READ it lol. Maybe someone could write this? They could name it The Taxxon Chronicles, which shows how taking the Taxxon homeworld ended the war.
