It's been quite a while since I read this book, but I just finished the second installment so I wanted to write the summaries in anticipation of the 3rd book's release. This will just be a vague summary since the first book isn't fresh in my mind.
Jacob is a 16 year old rich kid who goes with his dad on a trip to Wales, where their ancestry is located, on a "bird watching" expedition. His father is an author and Jacob says that his dad always gets obsessed with topics but then never completes what he starts.
Jacob is very close to his grandfather, and when he gets a call from his grandpa that he is looking for his guns to "kill them", Jacob rushes to his grandpa's house because he's afraid he will hurt himself since they all assume he is senile.
When Jacob reaches the house he finds his grandfather in the woods and sees a huge creature looming over him with his grandfathers insides torn out. Before his grandfather dies, he tells Jacob "Go to the island. Find the bird in the loop on Sept. 3, 1940, on the other side of the old man's grave."
It's at this point that he goes on the trip to Wales with his dad, thinking he will try to make sense of his grandfather's death by going to their family's homeplace.
His grandpa always told him stories of fantastical creatures and children who were "peculiar" and could do things like make fire from their fingertips, but Jacob assumed they were just stories until he saw the creature.
When he gets to Wales, he does end up finding the peculiar children and Miss Peregrine, who is their leader and one of many "ymbrynes" (pretty much a powerful witch who can turn into a bird and protects peculiars) by going through a swampy area into a type of crypt which comes out into another dimension where they all live.
Miss Peregrine ends up being taken by wights, who are beings with white eyes that look human but work for "hollows" or "hollowgast", which Miss Peregrine explains used to be peculiars who tried to overtake the loops and become more powerful but their plan backfired.
After a close escape from Jacob's psychiatrist from back home (who also turns out to be a wight but Jacob kills him), the children save Miss Peregrine but she is now in her bird form and cannot change back due to a spell cast upon her.
The peculiar children tell Jacob that he must help them to save Miss Peregrine since he is the only one who can actually see the hollowgast. He agrees to stay with them in their loop instead of returning home.