Area 7. You face off against ZODIAC Virgo, who has previously toppled Cancer and then wipes out Human Virgo. Suddenly, things get worse when he unleashes a No-Holds-Barred Beatdown on your ship, the Phoenix, wiping the ship's Life Meter and killing the pilot...but then the Phoenix reawakens as ZODIAC Ophiuchus and its AI kicks in, now with wings, stronger firepower, and an infinite-use shield, and you proceed to curbostomp a fleet of backup ships and then beat the snot out of Virgo.
Between Areas 7 and 8, ZODIAC Ophiuchus obliterates ten other ZODIACs by itself. Unfortunately, the awesomeness is severely subverted by the extreme damage the battles cause to the Earth and humanity, and Ophiuchus's programming doesn't care, only concerned with destroying its targets.
The Final Bosses, ZODIAC Libra and two Kamui fighters. One of the best moments is when Libra fires a massive laser at you and the two Kamui fighters (or one if you managed to wipe the other out). While the two Kamui loses their shields gradually and explode spectacularly, Ophiuchus's shield is, once again, completely unfazed. Libra tries to hit you again and...cripples itself, losing a significant chunk of its Life Meter.
It's very possible to kill Libra before it even begins its final attack phase. The opportunity to do so occurs during its Teleport Spam drone phase, which has blue bullets you can use the "photon blaster" attack on to pierce Libra's shield, damaging Libra. Defeating normally gets you 1 million points, but defeating him through photon blasts will net you a whopping 4 million due to the reflect multiplier.