WMG / Puella Magi Madoka Magica Portable

Homura will discover that Ultimate Madoka is the best possible ending.
In the game; Homura will be able to jump from Pre-Anime to Post-Anime timelines upon "unlocking" them, and even if she's able to save all of the cast and beat Walpurgisnacht, the very nature of Puella Magi/Witches means they don't have long to live anyways. Even if she does so and prevents Madoka from becoming a Magical Girl; Madoka will tell her she doesn't want to be alone when they eventually die/go witch in a few short years.
  • Her final ending will be like Halo: Reach, her fighting an infinite amount of spawning Manjuu Demons in the Wasteland until she dies or ascends; and then goes to be with Ultimate Madoka.
    • Confirmed: "After winning the game, you will always end up getting the anime's ending (whether Homura fights alone or with one of the girls as a team). During the wasteland scene, Homura will only have to fight the Demons until the ending music (Connect) ends."

Homura's True End was one of the canon timeloops.
It lasted for a few months, maybe a year... then some catastrophe hit, Madoka was forced to contract and eventually become a witch, and Homura couldn't do anything as her shield was out of sand. Homura had nothing left to do but reset the timeline.

As a Mahou Shoujo, Itzli was a foreigner
This is another interpretation on what an alien is-being from another country.

The reason why Walpurgisnacht cannot be defeated in the Bonus route
Walpurgisnacht is a collection of witches join together. In the Bonus route there was a bigger outbreak of witches in the halfway point. Remember the stockpile of grief seed that Kyoko gotten? This outbreak and the huge amount of grief seeds lying around joined with Walpurgisnacht.