Thanks to one of the research tasks I had previously carried out (into the theme of death in media aimed at a younger audience), I'm happy with the general concept for the story that I have created for this project.

I didn't want the story to be too heavy, as the comparable products and influences for me personally were games such as Super Mario Odyssey (2017), where there is an apparent story (shown with cutscenes) but the main focus is gameplay, with the cutscenes primarily shown at the start and end of levels.
However, so I can experience writing a story/script, I still intend to include differing events for the different islands and introduce new characters on each island, so there is some story that's apparent.

For this project, my group have decided that we will aim to create the first two levels of the game. meaning that levels/islands 3,4,5 and 6 will not be created (but still planned). However, the whole story/script will be created by me, as that's one of the main tasks of my role.

During one of the earlier stages of the project, I went through a number of story concepts. There were quite a few concepts I liked the idea of, but I eventually narrowed the concepts down to two different concepts (one being the current concept, and the other being the where the father is the antagonist) that I was happy to use for the story. The general outlines were developed to a point where the beginning and end were shown, and then these two concepts were voted on. After carrying out further research into my audience with my surveys, I feel as the decided concept was the more effective concept, as it makes use of a happy ending. The concept below is the further developed version of the winning concept

Below I have divided the story outline into two sections. Section 1 states the beginning of the story/the story of the first two levels, that we aim to include at the game shown at the exhibition, and then section 2 shows the story outline of the remaining levels/the game and story conclusion, which will not be created/implemented into the game being made.
The story of this section of the game is somewhat likely to go through some changes throughout this, and the next section of the project, but for now this is the story.

Section 1 Outline:
The story begins with the protagonists home island being attacked/invaded by the antagonists minions. While trying to escape and fend off the enemies, the protagonists mother is fatally wounded, which leads to hear death. With her last breaths she tells the protagonist to live on, and gives the protagonists a note and a fragment of a map (this note stating that the map was left by the father of the protagonist who has been missing since before the story takes place).

After the island attack is ended, the protagonist buries his mother on the island (most likely occurring during a part of the game/story that isn't shown/ a timeskip) and plans to leave the island. This being where the first crew member is introduced. As the protagonist has no boat, and is aware of his situation, a family friend of the protagonist offers to come along with the protagonist, lending both himself and his boat. Both characters then sail away from the first island, to the island shown in the map fragment.
 

Both characters now arrive at the second island, being a jungle desert island. Upon stepping in the island, the protagonist spots a group of enemies chasing after a small octopus, and decided to intervene, leading to the octopus being saved. The octopus then, out of gratitude and admiration, decides to follow the protagonist and help him complete his map quest (becomes the sidekick). 
The sidekick then informs the protagonist of some ruins that are located on the island, and states that the map fragment he's looking for could possible be located there.
After adventuring to the ruins, and solving the island puzzle, the map fragment is 'unlocked' and can be obtained by the player (this unlocking passage to the next level).

Section 2 Outline:
After previously obtaining the 2nd map fragment and travelling to the next island, the crew (now consisting of out protagonist, the 1st crew member/navigator, and the octopus sidekick) arrive at the next island, which is an antarctic-like frozen island. Upon arriving to the island, and entering the town/settlement that's located on the island, the protagonist is encountered by an doctor seeking help. He introduces himself and the problem at hand, being that there's people who are sick/injured on the island, and then explains that he requires the help of someone to go to a section of the island that's occupied by mechanical minions to find/collect some medical herbs that he can use to cure the sick/injured. The protagonist agrees to help this man, and set of to find the herbs (and also defeat the enemies on that section of the island).
Upon collecting the herbs and returning to the doctor, he thanks the protagonist and gives him a hint to where the the map fragment (inside the islands ruins) could be located.
Then just like the other islands, after finding the ruins, completing the puzzle and obtaining the map, the player once again can return to the ship and travl to the next island.
However, upon returning the the ship to travel to the next island, the protagonist is once again encountered by the doctor, who wishes to join the crew to travel to other islands to help those who may also need medical help, but to also help the protagonist during his dangerous journey. The protagonist, having no reason to decline, accepts the doctor to join the crew. Then (when the player decides to leave) the next island can be traveled to.

During the journey to the next island the protagonists ship is attacked by the antagonist (mecha shark) as he (the shark) attempts to eat the their ship. The shark fails to eat the ship, but does manage to take a bite/chunk out of the ship, causing it to become shipwrecked on the next island. The crew wake up on an uninhabited, mountainous island , and realise that their ship is too damaged to repair. The crew decide to stay with the ship, and try to see if there's anything that they can do, while the protagonist goes off to find the next map fragment (which after adventuring to the highest point of the island, is found to be inside of the ruins behind the waterfall. Upon solving the puzzle of the ruins and obtaining the map fragment, the protagonist returns to his crew to see if they've managed to find a way off of the island.
As the protagonist returns, a pirate ship is spotted on the horizon, approaching the island (in hopes of looting the beached ship). Upon arriving on the island, and leaving their ship to check what loot the beached ship may hold, the protagonist and his crew sneak onto their ship, and steal the boat (this could be likely to change to the protagonists crew fight the actual pirate crew, and then upon defeating them steal their ship).
Now with the stolen ship, the protagonist and his crew make their way to the next island.

As the crew arrive at the 5th island they discuss how the ship is running low on cannon ammunition, and they should probably try to find someone/somewhere on the island who sells them, as when they go back out to sea they will once again run the risk of encountering the mechanical shark/antagonist (foreshadowing to the events that actually will take place). The protagonist travels into the town and is required to look for someone to buy cannonballs from, and while doing so finds a woman who specialises in guns and cannons. Upon asking to purchase cannonballs, the woman asks why the protagonist wants them, and so the protagonist explains his crews encounter with pirates and the mecha shark. After hearing this she asks to meet with the protagonists crew members. Upon seeing them, and noticing that they're lacking in terms of cannon skills, she becomes determined to join to protagonists crew to help with his journey, but also with the hopes of meeting with the mecha shark (as in her backstory, she has also lost people who were precious to her, and wants revenge against the shark). The crew discuss how in terms of cannon skills they're lacking, and so it is decided that the woman will join the crew. After this, the protagonist is still required to go and find the final map fragment (which is located in the ruins within the volcano), while the crew stock the ship with cannon supplies.
Once the protagonist finds and obtains the map fragment, all of the pieces of the map have been collected, and the final island/location is shown.  The protagonist then returns to the ship, and the crew set sail for the final location of the map.

The crew travel to the location shown on the map, but upon arriving they aren't met with an island, but are instead met with a ship graveyard. But it's not just any ship graveyard, it's the mechanical sharks hunting grounds. Once again the protagonist and his crew are attacked by the mecha shark. Although they now posses a better ship and a crew member who specialises with cannons, the protagonist and his crew still fail to fend off the shark, and are eaten along with their ship.
Luckily, the ship only sustains minimum damage and the crew only receive minor injuries.
The crew, along with their ship, now find themselves inside of the sharks stomach. Shortly after being eaten, the crew are encountered by a man, who ends up being the protagonists father. This finally explaining the reason he went missing (being that he himself also encountered the same fate as the protagonist), but also concludes the protagonists main objective of wanting to find his father. However, they still need to find a way out of the shark. The father explains that since their ship was eaten but remained in a reasonable condition, he could fix and even upgrade it if the protagonist can find the required parts from other shipwrecks inside the sharks stomach (this becoming the collection dynamic for the level). Upon collecting all of the requested parts, the father manages to repair and upgrade the ship. The crew once again board the ship and, with the upgraded cannons, blast out of the sharks stomach. The enrages the shark, as it just took damage, but also lost it's meal, and so attacks the protagonists ship once again. This being where the final fight between the protagonist and his crew and the antagonist occurs (boss fight shown by gameplay).
Upon defeating the boss, the antagonist sinks into the ocean, and the protagonist and his crew sail of into the sun set, with all of the crew having completed what they set out to do.