Chapters:
0:00 Intro (all channels)
0:08 Square 2
0:59 Square 1
1:49 Square 1 and Square 2
2:40 Wave Pattern and Drums
3:31 PCM 1 and PCM 2
4:22 Square 1, Square 2, PCM 1, and PCM 2
5:13 All Channels

This is an oscilloscope deconstruction of VS. Alpha (VS. プロト) from Mega Man Battle Network 3.

Notes:
In Japan, the final boss Alpha is known as Proto (プロト). Note that in Japan, ProtoMan is known as Blues, so there is no conflict between these two names.
Like the final boss themes in MMBN1 and MMBN2, VS. Alpha is a remix of this game's boss battle theme. In this case, it uses Boss Battle's motif with a slower tempo, and with some new phrases added in.
The PCM channels are a lot more prominent in this song than in Boss Battle. The last sample in PCM 2 (4:08 - 4:21) reminds me of Mega Man Zero's soundfont.

What do you think of this deconstruction? Let me know in the comments.

Tools used:
Foobar2000 v2.0
VIOGSF (foobar2000 component, unzip and place the files directly in the components directory for foobar) -- used to rip square channels
agbplay -- used to rip PCM channels
Corrscope -- used to generate oscilloscope visualizations
Kdenlive -- used to edit the video