When the elements fused with the Mane 6 it caused their brains to not function at full capacity, the effects could lead to becoming mentally challenged, unable to perform basic tasks, failure of several body systems, ADD, ADHD, OCD, and insanity (this would explain Pinkie and Fluttershy's behavior). They were immediately sent to containment in hidden facilities until further research could be done. As the months went on more and more objects were sent to these facilities for study and research and they required more staff to handle them.

During this time, Dr. Bright was transported to Equestria, and within weeks he was able to become a resident in Ponyville. He wouldn't talk to anybody about where he came from and nopony was able to find any record of him prior to coming to Ponyville.

Princess Celestia, having heard about Dr. Bright through word of mouth, requested an interview with him in Canterlot. She decide to use a spell in order to see his past, in which she found out that he was from another world and that he worked for a secret organization. Celestia, seeing this as an opportunity, asked Dr. Bright to join their organization that was studying the Mane 6. Seeing as how the idea of this organization reminded him of the SCP Foundation, he decided to join.

After approximately 12 months of him working at the foundation, he became one of the Senior Staff and had proven to be very useful with his studies on the Mane 6. Dr. Bright was the pony who also gave the organization its name, the LTF Foundation.

When Rainbow Dash's element fused with her she became simple minded. She was able to perform basic tasks like sleeping and eating, but she can't seem to acknowledge any other ponies. During a containment breach, Rainbow Dash escaped the site, and went into the Everfree Forest for an unexplained reason.

Nobody heard from her for about two months until one day she suddenly emerged from the forest, but she wasn't the same. She had corrosion all over her and her attitude was increasingly aggressive. She also somehow gained the ability to walk through walls and take ponies into a "Pocket Dimension". When she emerged from the Everfree Forest, she immediately went to Ponyville and began causing havoc and attacking ponies. Foundation personnel quickly got to Ponyville to attempt to stop her. They found out that she's attracted to the sounds of someone screaming in pain, so the lure subject was created. Using this, they were able to get her back in her containment chamber, they installed electromagnets on the chamber in order to keep her there.

Scootaloo was one of the unfortunate ponies who were attacked by Rainbow Dash when she went into Ponyville. She was the only pony who made it out of the pocket dimension alive, but she didn't come out the same. Many of her body systems were not working but she was still alive, she doesn't require any sleep or food. Her speed increased to approximately 30 miles per hour and somehow developed echolocation, resulting in her being able to time her movements in order to stay out of someone's direct line of sight and remain hidden from their view.

When Twilight's element fused with her it cause her to develop OCD, she was constantly trying to gain more knowledge and build strange objects. During a containment breach, she managed to escape the site and run back to her home, where she built a giant machine that could refine items depending on what the dial on the front is set to. She also infused magic in it in order to make it sentient. Shortly after she built it, the LTF Foundation found her and took her back to the site along with the machine. As of now, Twilight is still the top priority in getting "cured".

The Crystal Heart was damaged during the changeling attack and became "broken", in a matter of speaking. It was taken to the LTF Foundation to see if they could do anything in order to "fix" it so that it could possibly supply the crystal empire with power again. After about 2 months of testing with it, they got it to function, but not the way it should. Whenever someone touches the heart they will be teleported to a 'Crystal Dimension', this dimension is composed of a crystal road with white fog everywhere, along with giant crystals all over the place. This dimension also contains hostile entities like shadow monsters cough* Lost cough* and other unidentifiable creatures, after being in the dimension for approximately 3-5 minutes, you will teleported back to the heart's location.