Alpha

Alpha, known in Japan as Proto (プロト), is the final boss of Mega Man Battle Network 3, a defections program that takes the form of an armored mass of a slime-like substance.

History
Alpha is the first Internet created by SciLab in a top secret project by Tadashi Hikari. It was developed as the basis for the current Net community. One day, all of the devices connected to Alpha malfunctioned, and the researchers thought the problem was the "AutoNavi" that was developed at the same time in another project. SciLab reacted strongly against the man who developed the AutoNavi, Dr. Cossak, and decided the Navi had to be deleted. He was held in custody, and the Navi Elite Corps deleted the Navi, but they didn't know that the Navi (later revealed to be Bass) survived. They thought the deletion of the Navi would solve the problem, but after that, the most devastating net-accident in history occured: All devices connected to Alpha were destroyed. It was later figured the AutoNavi was not responsible, but Alpha itself, which was riddled with bugs and gained a level of intelligence (more like instinct) around that of an amoeba. Alpha crept into all devices connected to itself and absorbed all manner of NetNavis, programs, and others, like a giant amoeba devouring all Cyberworld. A week later, it had devoured everything, and SciLab took advantage of its bloated state to capture it. Tadashi Hikari stopped it by installing a program called "Guardian" into Alpha's core, and SciLab locked it with four TetraCodes. All the Net society was brought to a halt for 6 months. This event was known as "The Alpha Revolt".

Years later, in Mega Man Battle Network 3, the WWW managed to steal Alpha from SciLab to use in Wily's "Cybergeddon" plan to destroy the Net society. Wily began decoding Alpha and started havoc by using AlphaBugs to control machines, starting by machines from the Army systems around the world. Lan's father tracked the WWW base at a place known as "The Demon Waters", a part of the ocean full of "Demon Currents", named due to the ferocious currents and whirlwinds. When Lan reached Wily, he had already decoded 80% of Alpha. Wily enters the network using the Pulse Transmission System. Lan and MegaMan uses the Pulse Transmission and Full Synchro to go after him, but Wily awakened Alpha with Bass' help to destroy the "Guardian" program. After MegaMan defeats Bass, Wily reveals he wanted Gospel to create a copy of Bass so he could destroy the "Guardian", and expected he and MegaMan to destroy each other. Alpha devours Bass and Wily, and the player fights against Alpha.

After defeating Alpha, a door appears, where it contains a file with the shape of a room from SciLab in the past and a data of Tadashi Hikari's personality, who monitors the Guardian and avoids Alpha's reawakening. With the destruction of Alpha and the Guardian, Tadashi was also going to be deleted, and he gave a encrypted message to Lan give to Yuichiro before the program started to fall apart. While leaving, a part of Alpha that was still alive swallowed MegaMan and Lan, and MegaMan overloaded himself to save Lan, presumably destroying himself. Lan later gave the message to his father, and Yuichiro reveals Alpha wasn't deleted until now because of the data of Tadashi. Months later, Yuichiro managed to read the encrypted message and was able to rescue MegaMan from a place Alpha could not touch, where Tadashi's personality data was stored. As this data of Tadashi doesn't appear in other games, it's believed he had to remove his data to store MegaMan, but there could be another possibility. In a sidequest, it's show Bass somehow managed to survive, but had amnesia. Shortly afterward, he meets Gospel, and they merge into BassGS.

Power and Abilities
Alpha itself is a powerful foe. As its arms are disconnected from its body, it can attack with them both down columns and rows. It can sometimes turn into a golden arm. Vulcan guns are concealed within its shoulders that can follow MegaMan across the battlefield. It also has a powerful eye laser that attacks the central panel and cracks the adjacent ones. On top of that, it can also use a lightning attack on the top and bottom rows and launch a missile to strike the back column when it explodes.

Its only weak point, its core, is covered in a gelatinous substance that must be peeled away first. While any attack can work on it, rapid MegaBuster shots work best to conserve Chips to inflict damage. Eventually, the goo will restore itself and must be peeled back again.

Attacks
Alpha can only be damaged by hitting the center until the substance covering the core vanishes.
 * Machine Gun: Alpha shoots from two machine guns summoned from its shoulders.
 * Break Laser: Alpha fires an laser to the closet enemy column that breaks every surround panels in a cross order.
 * Alpha Arm: Two of its arms constantly de-attached from the body and homing towards enemy.

AlphaBug
AlphaBug and ???? are enemies from Mega Man Battle Network 3 related to Alpha. All those enemies can regenerate fast, and they attack by trying to absorb MegaMan.

Trap
Inside the four robots from Wily Castle there are invisible puddles of Alpha that acts as traps. If MegaMan steps in one, he will return to the last "checkpoint". They are only visible with the "Alpha" program for the Navi Customizer given by Lan's father in one e-mail.

Trivia

 * Alpha bears a resemblance to the deletion program D-Reaper and the Mother D-Reaper form from the anime Digimon Tamers.
 * Alpha is likely based off of Green Devil as they share the same slime like body and weakness in the middle of the slime.
 * Alpha's original name, Proto, could be based off the fact that it was the prototype version of the Net.
 * Alpha's english name, Alpha, could be based off the fact that it was the first (Alpha not only being the first letter of the Greek alphabet, but is usually used to mean first just as Omega is used to mean last) version of the Net.
 * Alpha's name was likely changed to avoid confusion with ProtoMan.