Crystal City was the home of Cybertron's scientific elite. Shockwave worked there, as his innovations in stressed-crystal material allowed the large-scale usage of it in the city's construction. He was made to leave when his combination experiment, Bruticus Maximus, failed. Before the war, Soundwave sent Frenzy and Rumble to look for the Matrix of Leadership within the city. They overheard plans to reactivate Omega Supreme, Guardian of Cybertron's artifacts, as well as information on the Code Keys and the Plasma Energy Chamber that became useful during the final days of the war.
It was destroyed in the fourth offensive of the war, as Shockwave returned with a vengeance by unleashing his perfected combiner, Devastator. Devastator loomed over the Refracting Gardens and smashed open the wall, allowing the Decepticons to flood in. They took their time, smashing each and every object and piece of architecture. Watching on the Communication Grid, Alpha Trion remarked the dazzling display of light and colour as Crystal City collapsed was the most beautiful thing he had ever seen. Some scientists managed to get out of the underground laboratories, taking some of their research.
In the aftermath of the battle, Shockwave set up camp at Crystal City and reactivated Bruticus. The Geosynchronous Energon Bridge below the ruins also became of strategic importance in the war's final days. Transformers: Exodus
Vertebreak was once a member of Crystal City's science council, and studied surgical techniques from other civilizations. Unfortnately, he used this knowledge to advance his horrific cyber-grafting experiments, which got him kicked off the council and imprisoned.