Basically Nobita has a dream/premonition that these aliens are going to invade. He, Shizuka and Doraemon are outside at night, stargazing or something if I recall or maybe looking to intercept the aliens. The aliens in question turn out to be microscopic and they're targeting Nobita, but I think he sneezes or spazzes out or something and pushes Shizuka onto the floor. The tiny ship falls into her mouth instead of his. They part ways and go home to bed.
Nobita gets a call from Shizuka's mother I think, saying she's suddenly fallen ill. Nobita and Doraemon then use the door gadget thing to teleport to Shizuka's room, where's she laying in bed shivering with a fever, sneezing. Nobita recalls his premonition and thinks he saw something fly into Shizuka's mouth earlier, so Doraemon uses a gadget to see inside of her. They discover the alien ship in her stomach, so Doraemon pulls out a syringe gadget to try and cure her. The antidote flows through Shizuka's body wiping out the aliens it touches, but they manage to safely withdraw onto their ship.
Left with no other alternatives, they use the teleporting submarine to go inside Shizuka and fight the aliens themselves. They just teleport inside her stomach, nothing fancy. They sneak onto the alien ship, which is firing at Shizuka's stomach walls, causing her to sneeze frequently because anime logic. Basically they work their way into the ship and manage to sink it, escaping into their sub as a mixture of what I'm assuming is Shizuka's stomach acid and the antidote stuff floods the alien ship. They float above the stomach acid and watch the ship sink. There's no explanation of how they got out, we just time skip to Shizuka in bed the next morning feeling better.
It ends with a bit of a vorish undertone as Shizuka has her own premonition/dream where she opens a box of sushi and finds a tiny Nobita trapped and squirming in the food, which then correlates to the real Nobita opening his wardrobe(?) and a bunch of stuff falling out on him and squishing him.
I
think I'm remembering that right