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The first fic is awesome. The second one is "awesome," and those airquotes are massive. Why? The villain. More specifically, the Villain Sue, who mixes in traits of Sympathetic Sue and Einstein Sue. And here's a sampling of her sueishness: badass enough to kick voldemort's ass, a scientific genius (enough to give Petunia Dursley magic, Moaning Myrtle a living body, build an underwater base, a high-tech prosthetic arm for herself, and even have an Archaeopteryx as a familiar), went through a bad childhood (she got beaten because she talked about science in a religious school). has phazon superpowers. is connected with major canon characters (friends with Lily Potter. loving snape (who marries her later on!). has a vampire friend who was madam olympe's guardian. and close enough to dumbledore for him to confide to her that he's gay). there's more of course, but the word count keeps me from detailing it all. The fic does have its share of genuinely awesome moments, but she's too big a part of the story to ignore/forgive.
You wouldn't think a crossover between two series as different as Harry Potter and Metroid would work, but it does. I'm a fan of both series, having read every HP book, seen every movie, and played every Metroid game and almost beaten them all, and I have to say that the way the two mesh here is indescribably good, considering that the two have nothing in common.
An important thing to note about this series, being a crossover, is that the two series it makes use of are remarkably well-balanced. Many crossovers are guilty of making the characters from one series vastly superior or more powerful than characters from another. Whether this is realistically true or not for those series, it doesn't make for good storytelling. It's clear, however, that both the Potterverse and the Metroidverse are equals here.
Regarding the story itself, the author ensures that the stories, for the most part, fit well into the established canon of each series. If you wanted to, I imagine you could start reading Order of the Phoenix, put it down where Fusion of Destinies begins and read the fic, and then pick back up right where you left off, and the stories would flow into one another seemlessly.
There are two main styles of storytelling present throughout both fics. One of them is very Potter-esque, telling about the day-to-day lives of the cast while piecing together an over-arching plot. The other brings to mind the exploration of isolated environments typical to the Metroid series. In this way, different portions of the story are able to convey the same atmosphere that a legitimate entry into each series would likely have.
The parallels between Harry and Samus are excellent. Both of them are the heroes of their respective societies, orphaned at a young age, destined to fight for peace. The sibling-like bond they develop is touching at times, and it's a nice change from the shipping and drama you typically see a lot of in the HP fandom.
The villain of the second fic is often accused of being a Villain Sue, and to some extent it's true. There's not much she can't do, and she wears a friendly face and has otherwise noble goals. But to me, this actually makes Harry and Samus all that much more compelling as heroes. Offered everything they could dream of, they refuse to turn on their principles, and that means a lot.
One of my all-time favorites for sure.
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