From Lylat Wiki, your source on Star Fox information. By Fans, for Fans.
The Anglar Emperor (アングラー皇帝, Angurā Kōtei) is the leader of the Anglar race, and the primary antagonist of Star Fox Command. Originating on Venom, he appears as a final boss for several missions, and pilots a large serpent-like vehicle called the arrowhead. In some of the final missions, he becomes a very large angler fish, capable of taking the player's ship into his mouth, similar to Andross's ability in Star Fox 64. His three admins are Zako, Zazan, and Octoman. The Anglar Emperor resembles an anglar fish.
The Anglars made their existence known sometime after Star Fox: Assault, and launched a large attack against the system. The Star Fox Team had disbanded, and without them to defend Lylat, the Anglars quickly gained the upper hand, making it as far as Corneria. Near the end of the war, Star Fox Team was re-formed, and began decimating the Anglar Forces. Depending on the player's choices, The Anglar Emperor met his end at the hands of either Star Fox, or Star Wolf.
During the first phase, against the Arrow Head, it has to be blasted away section by section. It can only be hit when it is on the same floor with the player, and since the player cannot switch floors a useful tactic would be using Smart Bombs. As the player breaks off sections of the creature, the sections drop off to the bottom the room and will attempt to shoot the player down with lasers. Once enough sections are damaged, the remaining parts will align themselves tic-tac-toe style and attempt to ram the player. They can be blocked by shooting the sections or by rolling. This phase ends when the head is destroyed. In the main path, the battle ends here, since the player is fighting him in space and not on Venom. Otherwise, the Emperor will flee into the Venom Depths, and you will fight him "on rails" without a time limit.
Three pieces (which seem to be of the destroyed Arrow Head) will surround the Emperor and the player has to destroy them. Once that happens they will turn red and the Anglar Emperor will start attacking. The player has to shoot him on the esca (the antenna like thing on his head) and his life will begin to decrease. Once he takes enough damage, the player will have to deal with girders in addition to his normal attacks, and the girders will keep up until the player hits the pieces enough times as before. This part repeats until the battle is won, though it shouldn't take but one or two loops of this pattern to finish him.