Marahute thanks Cody by taking him on the ride of his life, and gives him a feather (which results in Cody hugging her head as shown in the picture).
Before that, when Marahute shows Cody her nest and he asks if they're due to hatch soon, she coos and fluffs up her feathers. Without uttering a single word, it's apparent that she's quite happy.
Cody is kidnapped by McLeach and the boy is dragged away with no other human knowing what has happened and no help will ever come. However, one mouse begs to differ as he rushes to a mouse radio transmission station to start a message relay to New York City to alert the Rescue Aid Society. In this sequence, you see a whole network of mice who have dedicated their lives to ensure that for the forgotten and oppressed, help is on the way.
See the scene here. The heartwarming turns funny when you realize that the Rescue Aid Society has absolutely no problem with usurping proper channels to get their message through. Who cares if dozens of humans are confused at all of these "R.A.S"'s popping up on their screens if a child can be helped? Which turns to awesome when you realize that the RAS has hacked the U.S. military.
As mentioned on the Awesome moments page, the R.A.S. views a single child being abducted as grounds for an immediate international full scale Red Alert with only the very best agents even being considered for the job.
Wilbur initially refuses to fly Bernard and Bianca to Australia (or anywhere) due to the massive blizzard outside. The moment they confirm that a child has been kidnapped and they're on a rescue mission? He's ready to fly!
Wilbur: Kidnapped? Oh. That-That’s awful. Lockin' up a little kid. Kids should be free! Free to run wild through the house on Saturday mornings, free to have cookies and milk, and get those little white mustaches, you know? (lividly) Nobody's gonna take a kid's freedom away while I'm around! Nobody! You hear me?! Bianca: Does that mean you'll take us? Wilbur: Storm or no storm, Albatross Airlines... at your service!
A small, but very sweet moment: on the plane to Australia, Bernard and Bianca are sleeping. She wakes up, smiles, and wakes Bernard up by kissing him on the cheek.
This moment:
Bianca: Oh, Cody, you mustn't give up hope. Bernard is still out there.
Jake: That's right. If there's anyone that can bail us out of this scrape, it's old Bernard. (surreptitiously) Nice bluff, Miss B.
Bianca: I wasn't bluffing! You don't know Bernard like I do. He'll never give up.
Even more heartwarming when connected to the first film. Bianca has always believed that Bernard is capable of more than others (including Bernard himself) think he is, and he's always lived up to her expectations.
The last scene:
Marahute is flying everyone home. They're up above the clouds on a beautiful starry night, Marahute calls happily while looking back at her human friend, Cody hugs his body against her and does his own bird-like call in response, and Bernard finally manages the speech he's been working up to the whole movie:
Bernard: Miss Bianca, before anything else happens... will you marry me?
Bianca: Oh Bernard... [throws her arms around his neck] of course I will!
Right after this happens, the camera (and presumably Bernard's attention) pans over to Jake, who's been making Bernard insecure since they arrived:
. The heartwarming turns funny when you realize that the Rescue Aid Society has absolutely no problem with usurping proper channels to get their message through. Who cares if dozens of humans are confused at all of these "R.A.S"'s popping up on their screens if a child can be helped? Which turns to awesome when you realize that the RAS has hacked the U.S. military.