The song tells a story about a robot (Rin) made by a lonely scientist, but is missing a program unable to be made: a Heart. Some time after her creation, her scientist passes away, leaving her alone for several hundred years. She begins to wonder about her creation and makes a wish. She accesses the files that her creator had left and finally gains a Heart. In the process, she discovers what it's like to be happy and sad. With her new feelings, she gratefully dedicates all of the songs that she sings to her creator. In the end, the miracle robot had a short in her system and could no longer sing. However, she had a smile on her face in her last moments, resembling an angel.
Many PVs present Rin's scientist being Kagamine Len.
Toraboruta-P announced that on April 27th, 2012; (previously it's stated to be April 17th, but it was delayed) he will release his novel entitled "Kokoro"; a novel based on the song.
The novel is written by Katsuyoshi Ishizawa (the same writer who wrote for the Kokoro stage play); and illustrated by Nagimiso.SYS; illustrator most notable for his PV of "Roshin Yuukai" also a card illustration by redjuice. The price is 1,200 yen and was available for purchase in Amazon on April 27th.
A crossfade of the novel ("Kokoro" arrangement by Toraboruta-P and video by Nagimiso.SYS) can be seen on niconico and YouTube. A month after the novel was put on sale on Amazon; it was announced that the "Kokoro" Novel have sold out and could no longer be purchased from Amazon. There is currently no news of second waves of printing; however it has sold faster than expected.
A touching take on the ココロ story by Ema Arihara, showing the true intimacies the robot and scientist experience. A mix of the original song, piano arrangement and orchestral arrangement are played throughout the slideshow. It is considered the epitome of the "Kokoro" saga and the emotions it invokes. The doujinshi is available to read in pixiv.
One of the most popular and famous derivations of "Kokoro" is "Kokoro・Kiseki" composed by Jun-P and sung by Len.
"Kokoro・Kiseki" serves as a prologue to "Kokoro", telling the story of the scientist who created the robot in "Kokoro". Short after create the robot, the scientist realizes she is missing something important: her kokoro. Whishing to share happiness and sadness with her, he begins to work tirelessly at creating a heart for her. However, the time is running out for his life will eventually come to an end. As he begins to lose hope, a miracle (Kiseki) suddenly happens: he receives a message from the robot from the future, after she has created her own kokoro. The scientist obtains peace and passes away in tranquility.
Though there is no clue who the scientist is in "Kokoro" and despite in "Kokoro・Kiseki", Len is not directly portrayed as the scientist, after the release of Jun-P's work, many PVs depicting Len as the scientist were made.
There is also a mixed version "Kokoro" and "Kokoro・Kiseki". The songs switch between one and the other and eventually resulting in a crescendo of both songs finales being played in unison. As the melodies of the two songs were written to complement each other, the final effect is a complete and harmonious experience.
Description This version sung by KAITO and MEIKO follows the same story as the original "Kokoro" and "Kokoro・Kiseki", with KAITO taking the role as the scientist and MEIKO portraying the robot. Both versions originally existed separately but were combined in the same fashion as Rin and Lens versions to form a harmonious melody when played together.
The songs of the series are arrangements of "Kokoro" and "Kokoro・Kiseki". Suginohito and his group, who produced the series, changed the original lyrics and they are based on a fanfic written by Oshimaino-P. They announced the episodes of the series has nothing to do with the originals. 
Description This is a parody arrangement of "Kokoro. Rin was a genius "chemist" who developed "Lambda Organ", a nameless "creature" (KAITO). But it was still missing "kokoro" and it wished to know what is like to have it. After a few hundreds years, it causes a disaster.
ココロ・アナザー -ラムダオーガン- Episode ZERO (Kokoro・Another -Lambda Organ- Episode ZERO)
Suginohito (Rin, Len), Frozen Strawberry (mix)
Kagamine Rin, Kagamine Len
Description This song is an arrangement of "Kokoro・Kiseki" which tells why Rin, a genius "chemist", developed "Lambda Organ" in Kokoro・Another -Lambda Organ-. When Rin was born, her body was in stitches. She was able to be born alive, while her twin brother couldn't. But she had to stay in a biological clean laboratory alone all her life. Since she had lived in loneliness, she wished her brother had been with her. And she developed "Lambda Organ" (KAITO) and spent her last moments together.
Description This is an arrangement of both "Kokoro" and "Kokoro・Kiseki" which shows the alternative future of Kokoro・Another -Lambda Organ- Episode ZERO and it is dramatically different from Kokoro・Another -Lambda Organ-.