When a snake attack threatens his species with extinction, a sheltered kangaroo rat must embark on a perilous journey to unite his colony with another, 250 kilometers away.

To be honest I hadn't even thought of that. Perhaps...

Veagle was the name I gave them too! His backstory: He was captured by humans and kept illegally as a pet- had his wings clipped and can no longer fly. He escapes and comes across the hero in a moment of need. Due to his bad experience at the hands of humans he becomes a kind of 'right on, meat is murder' type character, although his animalistic instincts do creep in from time to time and he has to really restrain from eating the hero (he has his own mission to find the golden eagles as well)

Always love a crazy elder!

Bug's Life came to mind for me too.

Vegan eagle (veagle?) is nice but I wonder if it's straying a little close to the vegetarian sharks in Finding Nemo.

My thinking for the hero's mission- he has to persuade a group of golden eagles to fly the remaining colony south on their upcoming migration (the eagles would much rather eat them all)

both great pieces of feedback

Maybe there's an elder kangaroo rat in the colony who somehow came from the distant colony, but the others dismiss him as mad and say its impossible, but the hero believes him.

I was thinking along the lines of bugs life, where he goes on his own, meets some allies and returns. (There's a vegan eagle character in mind amongst others!)

Agree with Mike Pedley.

And how would a kangaroo rat know there is a "cousin" colony 250 k-i-l-o-m-e-t-e-r-s away?

There's something here for sure.

I don't think the snake attack can be said to threaten his species with extinction when there's another colony 250km away. It can threaten his colony, but we already know there are others. How does the kangaroo rat know there's another colony? Or is his quest to find others and he doesn't know if there are any more? Either way, write it from his perspective.

"A sheltered kangaroo rat must lead the desperate survivors on a perilous journey across the desert to find more of their kind after a vicious snake attack decimates the colony."

I can't decide if it's better for him to go alone and then cut back to the remains of the colony who are eagerly awaiting his return with reinforcements, or for him to have the responsibility of looking after everyone left. Go with the story you want to tell.

Keep going with this.

Hope this helps.