Logan and The Secret of NIMH is the fourth story in the Logan's Adventures series written by Logan "Hewylewis" Ridenbaugh and Bryce "The Wrestlemaniac" Kanyon and released in DeviantArt on December 18th, 2012.
Mrs. Brisby, a shy and timid field mouse, lives in a cinderblock with her children in a field on the Fitzgibbons' farm. She is preparing to move her family out of the field they live in as plowing time approaches; however, her son Timothy has fallen ill. She visits Mr. Ages, another mouse and old friend of her late husband, Jonathan, who diagnoses Timothy with pneumonia and provides her with some medicine from his laboratory. Mr. Ages warns her that Timothy must stay inside for at least three weeks or he will die. On her way back home she encounters Logan and his first mate, Popeye, and Jeremy, a clumsy but compassionate crow. They narrowly escape from the Fitzgibbons' cat Dragon.
The next day, Mrs. Brisby and her new friends discover to her horror that Farmer Fitzgibbons has started spring plowing early. Although Auntie Shrew and Logan help her disable his tractor, Mrs. Brisby knows she must come up with another plan. With the help of Jeremy and the boys, she visits the Great Owl, a wise creature living in the nearby woods, to ask for help. He tells them to visit a mysterious group of rats who live beneath a rose bush on the farm and ask for Nicodemus, the wise and mystical leader of the rats. During this encounter, The Great Owl appears to recognize Logan and informs him of a destiny he is set to fill.
Mrs. Brisby, Logan, and Popeye enter the rose bush and make their way down to the rats' home, where they are amazed to see their use of electricity and other human technology. They meet Nicodemus, Justin, a kind and friendly rat who is the Captain of the Gaurds, and a ruthless, power-hungry rat named Jenner. From Nicodemus, they learn that many years ago Mrs. Brisby's husband, along with the rats and Mr. Ages, were once part of a series of experiments at a place known as NIMH (which stands for the National Institute of Mental Health). The experiments had boosted their intelligence to human level, allowing them to escape easily. However, the rats have concocted "The Plan", which is to leave the farm and live without stealing electricity from humans. Nicodemus then gives Mrs. Brisby an amulet called 'The Stone', that gives magical power when its wearer is courageous.
Because of her husband's prior relationship with the rats (mostly with Nicodemus), they agree to help Mrs. Brisby move her home out of the path of the plow. But the first thing that they need to do is to drug Dragon to sleep, so that they can complete the move safely. Only mice are small enough to fit through the hole leading into the house; Jonathan was killed by Dragon in a previous attempt, while Mr. Ages broke his leg in another. Later that night, she successfully puts the drug into the cat's food dish, but the Fitzgibbons' son Billy catches her and convinces his mother to let him keep her as a pet. Rather than leave, Logan chooses to stay behind to rescue Mrs. Brisby while Popeye joins up with Justin to have the plan set. While rescuing Mrs. Brisby, who is trapped in a birdcage, they overhear a telephone conversation between Farmer Fitzgibbons and NIMH and learns that NIMH intends to come to the farm to exterminate the rats the next day. Logan manages to help Mrs. Brisby escape from the cage and runs off to warn Justin.
Meanwhile, Popeye and the rats are in the process of moving the Brisby home using a rope and pulley system during a thunderstorm. However, Jenner, who is strongly opposed to the Plan and wishes for the clan to remain in the rose bush, sabotages the ropes with his hesitant accomplice Sullivan, causing the cinder block to fall and crush Nicodemus, killing him and making it look like an accident. At that time, Sullivan feels extremely remorseful for letting this happen. Mrs. Brisby and Logan arrive and try to convince the rats that NIMH is coming and that they must leave immediately, but Jenner, angered by their claims, attacks Mrs. Brisby and attempts to take the amulet from her neck. At which time, Logan reveals himself as a Keyblade Wielder and tricks Jenner into handing Brisby and the stone to him in exchange for the keyblade (Only to discover it can never be separated from it's owner). Alerted to the situation by Sullivan (who later gets mortall stabbed by Jenner), Justin rushes to Mrs. Brisby's aid and helps Logan battle Jenner, who then finally admits to having plotted the sabotaging that killed Nicodemus to take over the group. As Justin manages to defeat Jenner by stabbing him, he addresses the other rats to prepare for their departure from the farm immediately. However, Jenner despite his injury, attempts to make a lethal blow on Justin with his sword, but the dying Sullivan saves Justin by killing Jenner with a throwing knife behind him.
Mrs. Brisby, Logan, and Popeye see the house sinking in the mud it landed in, but Justin and the rats are unable to raise it from the muck and Logan nearly drowns during the attempt. However, Mrs. Brisby's will to save her children and Logan gives power to the amulet, which she uses to lift the house out of the mud (Saving Logan as well) and move it to safety from the plow. In addition, they discover that Mrs. Brisby's courage has in addition bestowed her with a keyblade of her own. The next morning, the rats depart to Thorn Valley with Justin as their new leader and Timothy has begun to recover. Logan and Popeye prepare to leave when Yen Sid arrives to inform Brisby that her status as a new keyblade wielder puts her and her family at great risk, and will be required to reside on Yen Sid's homeland, where she will be trained to prepare for when the moment is right (In exchange for a cure for Timothy's condition). On their way back to their ship, Max, Logan and Popeye are surprised to learn that Justin has agreed to join Logan's team, provided he can safely return to Thorn Valley once his service is no longer needed. Jeremy also finds "Miss Right", an equally clumsy crow, and the two fly away together.
Little do they know, an evil Council has been observing Logan's progress during his travels and have big plans in store for our heroes.
- The Fantasy Adventure Team are briefly mentioned in this episode
- Saruman makes an appearance as part of an evil council, along with Professor Ratigan, Rothbart, Mirage, Jadis the White Witch, Emperor Palpatine, and The Horned King.
- Sauron and Unicron are briefly mentioned in this episode.
- Paying tribute to the late Elizabeth Hartman (Mrs. Brisby's voice actress), whose last role was Mrs. Brisby in the original film, Elizabeth was used as Brisby's first name for the fan series.
- In this episode, Logan recruits Justin as a member of his crew.