One idea could be that the Spartans from Halo and the Witches from Strike Witches team up to fight a common alien threat that has invaded both of their universes. The Spartans' advanced weaponry and combat skills combined with the Witches' magical abilities would make for an epic battle.
Perhaps a scenario where a Halo technology gets mixed up with the Strike Witches' world. For example, a Covenant energy source ends up in the Strike Witches' world and starts causing strange magical disruptions. The Witches then have to work with Halo characters who understand the technology to fix it.
A story could be about a Witch who gets lost in the Halo universe. She has to quickly adapt to the more militaristic and high - tech environment. Along the way, she meets Master Chief and they form an unlikely alliance. She uses her magic in unique ways to help him in his missions against the Covenant.