At the beginning of the film, Marlin and his mate, Coral are expecting 400 children, which are due to hatch soon. The two are discussing names for their children, when a barracuda attacks. While Coral disappeared, and most of the eggs perish, Marlin and one slightly damaged egg survive. Marlin chooses to name his remaining child Nemo, a name Coral had liked.

As Nemo grows, Marlin becomes very overprotective of him, in part due to Nemo's unusually small right fin, which was a result of the earlier attack. One day, Marlin reluctantly sends Nemo to school. At one point, thanks to the alert of one student, Kathy, Nemo swims out into the open ocean to touch a boat as a result of a dare, much to the horror of Marlin. Nemo is captured by a diver. However, the diver drops a mask which bears his address, though Marlin can't read it.

Marlin is able to obtain the help of Dory, who is able to read the address but has short-term memory loss, and learns that Nemo has been taken to Sydney, Australia. Marlin, along with Dory, sets out for Sydney in an attempt to rescue his son. At one point on their journey, Dory is injured by jellyfish. Marlin swims through the jellyfish and is able to rescue her. (He explains that since he lives in an anemone, he is resistant to stings.) Marlin soon passes out, and awakens on the back of a sea turtle named Crush, who is riding the East Australian Current (EAC). After Marlin shares his story with some young sea turtles, word of mouth soon reaches Sydney and eventually, Nemo.

Marlin eventually reaches Sydney's harbor by way of a Whale, after becoming lost in the polluted water. Nigel, a pelican who has heard of Marlin, and knows Nemo, takes Marlin and Dory to a dentist's office where Nemo was taken. There, they find Nemo, apparently dead (Nemo was actually faking it in an attempt to escape). Saddened, Marlin leaves for home, leaving Dory behind despite her claims that her memory is better with him. Later, while swimming through a fishing area, he hears a familiar voice calling out to him. He soon realizes that it's Dory and a still alive Nemo. Dory had met Nemo and soon remembered everything, leading him to Marlin. Marlin happily reunites with his son, but the moment is cut short when Dory is caught in a fishing net. Marlin watches as Nemo is able to successfully rescue her with skills he learned while in the tank at the dentist's office. Marlin had disobeyed himself and becomes less overprotective. The end of the film shows Marlin, along with Dory, waving goodbye as Nemo goes off to school.

Finding Dory Edit

In the sequel, Marlin, along with Nemo, accompanies Dory to the Jewel of Morro Bay, California, in her journey to find her parents, whom she suddenly remembers.

Marlin first appears in the flashback during the events of the first film worried that he lost his son after a boat (which is Philip Sherman's boat from Finding Nemo) zips above Dory's head. Soon as Dory swims away, she collides with Marlin as the adventure of Finding Nemo begins.

One year after Nemo's rescue, Dory is the next door neighbor to Marlin and Nemo, living in a purple coral bowl, similar to her original home in the Marine Life Institute. Marlin and Nemo are disturbed by Dory in the middle of the night who tell her to go back to bed until he gives up and gets ready for the day. The next day, Marlin, Nemo, and Dory go on a field trip to Nemo's class (much to Mr. Ray's annoyance) to a stingray migration. After Dory is knocked unconscious by a large flock of migrating stingrays and Dory decides to swim to the drop off to find her parents after mumbling the "Jewel of Morro Bay, California", Marlin refuses to go at first until Dory asks him if he's ever missed his family, which brings up memories of Nemo's capture. However, he begrudgingly takes Dory and his son with him as they go to see Crush and ride the current to California. In it, Marlin, Dory, and Nemo hang onto Crush as the three arrive into their destination in a sunken wreckage in Morro Bay, California where he and Squirt wish the three good luck into helping Dory find her missing parents.

Upon arriving in Morro Bay, he, Nemo and Dory arrive in a wreckage where hermit crabs keep shushing the three as they swim along and the three are chased by an enormous giant squid after seeing its eye and fearsome beak inside a crate. While trying to escape, Dory and Marlin are worried that the giant squid grabbed Nemo with one of its tentacles and tries to eat him with its fearsome beak as the two escape from the marine predator after the squid is stuck on a sunken crate while chasing the three. The squid is suddenly crushed as the three suddenly escape the sunken wreckage and arrive in the kelp forest in Morro Bay, California where Marlin tells Dory to slow down because the giant squid is crushed when it tried to eat Nemo.

Upon stopping in the kelp forest of Morro Bay, California, Marlin is worried that Nemo is injured after being chased by the giant squid in which he shoos Dory away after heavily expressing Nemo who is injured during the chase, leaving her insulted greatly and causing her to swim off in despondency. Upon arriving in the surface of the Marine Life Institute, Dory gets kidnapped by two volunteers of the Marine Life Institute, as the father-son clownfish duo goes on a quest to find her. After Dory is captured by a group of MLI rescue volunteers, Marlin is worried about himself that he should have never insulted Dory after escaping from the giant squid, upset that Dory is captured by volunteers of the Marine Life Institute.

Upon hearing two sea lions telling him to be quiet, Nemo suddenly attempts to ask but Marlin warns him that he should not talk to the sea lions, explaining to him that the two are natural predators that could pounce on them at any second. Nemo then explains to his father that the two sea lions do not have the chance to pounce at them while Marlin asks the two about the Institute in which the two explain that it is a fish hospital. Fluke and Rudder help the two clownfish get inside the Institute by calling a flock of loons, including their friend Becky. After Fluke introduces their friend to Marlin and Nemo, she begins to peck at Marlin; Fluke tells the loon to bring Marlin and Nemo to Quarantine and Marlin is suggested to imprint by looking her in the eye and do a loon call.

After Gerald brings a green bucket to Fluke and Rudder, Marlin suggests that he and Nemo need water as the two sea lions kick and shoo him off from their rock after inviting them and giving the bucket to them on their rock. Meanwhile, Marlin and Nemo board on the green bucket carried by Becky as she flies to help take Marlin and Nemo get to the Institute while the two sea lions wish them good luck into their quest to find Dory and help her find her parents. As the two clownfish are carried by Becky, Marlin is disappointed that Becky is confused and doesn't know where to find the quarantine area and accidentally leaves Marlin and Nemo on a branch, thus she starts eating popcorn that fell into a floor after Hank bumped into a girl who has a cup of popcorn while trying to get to the Open Ocean exhibit. The father-son clownfish duo, still in the green bucket, plan to approach Becky so that she could pick up the bucket again; however, the branch flings the two clownfish as they end up in a small tank outside a gift shop.

Upon ending up in the tank, Marlin and Nemo see Becky carrying the green bucket to the quarantine area's roof as Marlin tries to call Becky for attention to rescue the two, but Becky cannot hear Marlin yelling for help from him. Upon seeing a wind-up toy fish that resembles Dory, behind the two clownfish is a spray pool in which the two clownfish leap out of the tank as they leap on the nozzles launching the two and leading them safely to a tide pool exhibit. Upon arriving, Marlin and Nemo suddenly hear a clam who doesn't know who Dory is as they approach them. The clam explains to Marlin and Nemo that he did not have anyone to talk to for years until Marlin and Nemo ended up in the tide pool exhibit in which Marlin tells the clam that they can't stay for a while as the two need to continue their quest in helping find Dory. The clam tells the two clownfish to stay with him and talk to him for a while before the two can continue their adventure.

Marlin and Nemo later appear swimming through the pipes as the two approach Dory who finally find her. Marlin explains to Dory that they encountered a talkative clam in the tide pool exhibit in which Nemo explains that he and Marlin backed away from the talkative clam as the two ended up in the pipes. Dory suddenly guides the father-son clownfish duo to the parts where her missing parents would be and they would be excited after she finds them. Marlin then apologizes to Dory for being too harsh by insulting her and causing her to swim in despondency. Soon as Dory continues arriving at the area where she would find her parents, she and the clownfish duo end up in the quarantine area in which the two leap from tank to tank to find her missing parents, but one hits the three as they end up in a mop bucket in which Hank Lifts them up in a cup of water and brings them to a tank of blue tang fish. Upon encountering and asking the blue tangs about her parents, some of them explain to her that her parents are not in this area, leaving Nemo, Marlin, and Dory in worry. When Hank is worried that the truck is ready to depart for Cleveland and he brings Dory and then escapes from the MLI employees, Marlin, Nemo, the blue tangs, and the rest of the species of fish are later taken to the truck that leads all the fish to a permanent aquarium in Cleveland, leaving Dory all alone.

Marlin and Nemo are later seen inside the truck and some otters arrive inside with Dory to the rescue as Hank puts her in a tank where Marlin and Nemo are at where the two are happy that they met Dory again. Soon after the otters are shooed away by a truck driver and the traffic begins to move, Marlin suddenly calls for Becky's attention to rescue the two clownfish as Becky suddenly appears perching on Hank's head. Soon as Nemo and Marlin leap into the green bucket, Dory is suddenly abandoned as Becky brings the two to the ocean. Upon arriving back in the ocean, the two clownfish suddenly encounter Destiny and Dory's parents Charlie and Jenny. Marlin suddenly tells the two that Dory is still inside the truck while he tells Becky to return to the truck to rescue Dory. Soon as the truck prepares to leave for Cleveland, Marlin, along with Nemo, Jenny, Charlie, Destiny, and Bailey prepare to stop the truck again in which they suddenly miss the truck. Marlin, Nemo, Destiny, Bailey, and Dory's parents later see the truck hijacked by Dory and Hank being driven into the ocean by falling off the cliff freeing all the fish inside the truck while Dory and Hank fall into the ocean.

During the epilogue, Dory finds Nemo and Marlin, along with her parents and the school children by playing hide and seek as they attend a substitute class by Hank, Bailey, and Destiny. After Dory says goodbye to her parents, Marlin suggests to Dory to return home in which Dory tells her that she would look at the drop off in which Marlin, (who is anxious about her) doesn't think going back to the drop off is a good idea because he thinks Dory could be lost again. Dory tells him that she would enjoy the view safely. Marlin suddenly accompanies Dory looking over the drop off in which he finally relaxes against the drop off, praising her that she did it by finding her parents, sparkling one last flashback when Dory was a baby and her parents proudly praise her for following the trail of shells all the way back home to the coral, as the two allow her to play with the other fish children as she swims off happily. Back to her own mindset, Marlin and Dory are last seen watching the drop off view safely as Dory smiles feeling accomplished and satisfied about herself after finding her missing parents as she deems the memories "unforgettable".