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These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
The first time you fight the Mecha Penguinators. It's basically the equivalent of the Baron of Hell. Then you fight two of them at the same time. Then you fight the Mk-II version, which can only be described as the Penguin Cyberdemon. It helps that they were supposed to be the final bosses of TAGAP's first part.
The final Henchman fight in the sequel, before they get demoted to minibosses. First phase is a jet, which is more fast and frantic than the Helicopter in the first game. Then the Mutator Rig kicks in, and you get a fat, flying penguin that shoots rockets everywhere.
Megamania in the first game. It's basically a Boss Rush level, where you have to fight Pedro five times. And in the last fight he uses a One-Up, surprising the player.
The second part of Endgame in the sequel. The first part it kind of a cheap shot with a Scorpion, randomly spawning chaingun wieldingGiant Mooks and a miniboss with attacks that are difficult to completely avoid; all of this with heavy music and red lights to give you a sense of dread. The second part has much more upbeat music, gives you more supplies and, to counterbalance, a metric ton of various kind of enemies, including a Mega Penguinator Mk-II and a Henchman. Twice, intervallated by a fight with a Mecha Crawler with heavy backup. With the XBox's Ring in the background.
Demonic Spiders: Scorpions. They are invulnerable aside for their "eye", which is very small and is shielded when it attacks. And it uses a chaingun, which will destroy your health if you don't react fast enough... and probably you'll run into it the first time and won't have time to back up from the bulletstorm. Somewhat lessened by having relatively low health, being especially vulnerable of nailbots, and the possibility of sliding directly in front of it and under the bullets, since it can't shoot and adjust its aim at the same time.