It begns with the Young Avengers fighting a terrorist band, so business as usual for them. Then, the real Avengers show up. When one of the terrorists attempts to detonate a nuclear weapon, Wiccan stops him, but accidentally KO's all the terrorists with his magic. This reminds the Avengers of Wanda, the Scarlet Witch, prompting them to relate the tale of the House of M: An alternate world where mutants ruled, and which was ultimately undone when Wanda de-powered the world's mutants and disappeared. The Avengers suspect that Wiccan and Speed may be the Scarlet Witch's lost sons, given that they're roughly the right age and bear similar powers to that of the Scarlet Witch and Quicksilver. The Young Avengers agree that they should start looking for Wanda, which leads to disagreement between the Avengers and their junior counterparts over who should take part in the search. After the prerequisite squabbling, the teams split up and 'Wanda' is located in Transia, only for her to be revealed as a Doombot. This, naturally, leads them to Latveria, kingdom of Doctor Doom himself.
Wiccan, entering Doom's castle alone, locates the Scarlet Witch; unfortunately, she not only has amnesia, but is scheduled to marry Doom. While Doom interrupts Wiccan's explanations to Wanda, defeating the boy, Wanda is intrigued enough by what Wiccan had told her to escape with him. This leads, of course, into a massive fight outside of Castle Doom, featuring the Avengers, the Young Avengers, Magneto, and the Latverian army. Iron Lad appears and intervenes, taking Wanda and the Young Avengers into the past, before the events of Avengers Disassembled. Wanda's still an amnesiac, and - hoping to spur her memories - they take her to the Avengers Mansion, where Cassie disregards the rules of time-travel to hug her deceased father, Scott Lang, who's currently still alive. The appearance of Jack of Hearts marks the beginning of Disassembled, but this time his explosive second death does not kill Scott, and the event returns Wanda's memories to her. Wanda is stricken by the realization of what she's done, but Beast suggests that, if she caused such chaos with a spell, why not undo it with a spell? They get in touch with X-Factor to test the theory, and Wanda successfully restores Rictor's powers.
The X-Men show up, intent on executing the Scarlet Witch for her crimes, while the Avengers and Magnet arrive to stop them. To halt the battle between the two groups, Wanda uses her magic to put them all to sleep and returns to Latveria, where she says that she thinks it would be possible to re-power all the mutants in the world at once... with the aid of Wiccan and Doom, who agree to help. Patriot, however, objects, believing that Doom is planning to use the ritual for his own ends, and attacks in the middle of the spell, which sends it haywire and infuses Doom with Wanda's reality-warping powers. Now a beatific, megalomaniac giant, Doom is attacked by both the Avengers and the X-Men, apparently killing Scott Lang in the ensuing battle. Cassie attacks Doom, resulting in Doom killing her off for real. Wanda and Wiccan re-attempt the ritual, and when Doom attempts to gain even more power, it backfires on him and returns him to his previous, non-reality-warping state.
Doom no longer has the ability to alter reality, but neither does the Scarlet Witch, leaving them unable to restore the world's mutants as they'd hoped to do. In the aftermath, the Young Avengers dissolve as a group; however, they're later summoned to Avengers Mansion, where they are acknowledged not as Young Avengers, but as true Avengers.