Hey there, found this thread from browsing the Interwebs.
I got one that is a crossover of Transformers and Macross Frontier, so very imaginatively titled "Transformers: Frontier." It takes place two years after the events of the Macross Frontier finale, wherein the Cybertronian Civil War reaches the Vajra planet where the Frontier crew settled.
http://www.fanfiction.net/s/5348638/...rmers_Frontier
BTW, it bugs me that out of almost 100 fics for Mac F, somewhere around 90-something deal with shipping.