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The problem was that Anders couldn't heal Justice. Or, more specifically, he couldn't heal the corpse that Justice inhabited.
It's common knowledge that spirit healers can heal anything that has life in it. The problem was that corpses, by definition, do not have life in them. When they're inhabited by spirits, they're animated purely by magic. Unfortunately, because Justice had wound up inhabiting Kristoff's corpse without intent neither from himself nor the mage that had put him there, the magic that held him wasn't the kind that also prevented the corpse from decaying. Nor was it the kind that would heal any damage that happened to the corpse. And, for Anders to repair that damage, he would need to study the kind of blood magic that the Chantry had actually managed to prevent Circle Mages from discovering.
Anders supposed that as a Warden, he probably could find some sort of excuse to wander up to Tevinter to see if they had some sort of ancient blood magic from pre-Blight times that could help him. However, there were two problems with that:
1) Anders didn't have that kind of time.
2) Anders now had a Templar shadow again.
In the end, it seemed inevitable. Ser Rylock of the Templars had had an obsession with Anders specifically and keeping him in the Circle. Despite her clear transgressions, the Templars couldn't tolerate a mage killing one of their own. They couldn't legally bring him back under their authority since he became a Warden. However, that didn't prevent them from pulling strings to get a Templar into the Wardens and subsequently from manipulating someone higher than the Warden-Commander of Ferelden to make sure that Rolan was assigned to all of Anders' field missions.
When Anders had realized what was happening, he'd asked his fellow Fereldan Wardens to come with him. To their credit, they had tried, but Rolan was sneaky and behaved where they could see and that only served to make Anders feel crazier. The only comrade that had never doubted him was Justice. Unfortunately, that was because Rolan also had a problem with spirits inhabiting the corpses of Wardens.
Because Justice had no legal protection except for the tolerance of the Warden-Commander of Ferelden, Rolan felt like he could treat both Anders and Justice in a way that he felt they deserved. This meant using Justice as a meat shield and harassing them both with nitpicks on proper Warden protocol, which included bullying Anders into getting rid of Ser Pounce-a-lot.
This latest mission had been one of the worst. They'd been assigned to investigate a village destroyed by a Darkspawn raid. Their scout had found two trails: one that suggested a handful of villagers had escaped, and one that suggested there were survivors who'd been dragged into the woods. Anders and Justice followed the second trail, hoping that whoever they found only needed healing, knowing that it was more likely any survivors were beyond Anders' abilities.
When they arrived at the cave, there was only one survivor left, a ghoul of a woman, gnawing on an errant leg that had likely belonged to one of her companions. She growled at their intrusion; she was too far gone. Justice unsheathed his weapon, and she pounced on him.
The struggle she gave Anders' friend was one of the worst that he'd ever seen. If they had caught her sooner, before the Blight had progressed as far as it had, Anders could practically hear the Commander lamenting that this woman would've made a great Warden.
In the end, to stop her, Anders couldn't take the precaution he normally would with his fire magic, and it wound up burning Justice's body. Anders might have normally said beyond repair, but any damage done to Justice's body was beyond repair. Unfortunately, the damage the ghoul had done was far worse. The body was no longer usable.
Cradling the burned corpse that housed his friend, Anders wondered what he could do to make up for his mistake. He prayed to Andraste to show him the solution. Weeping, he refused to accept that this was the end for his friend. Justice meant too much to him. Before he'd met Justice, his only goal was to escape the Circle, and he knew deep down that he would've been content with only achieving that. It'd been Justice that shown him that as long as the Circle existed, he could never be free. That everything he endured up until this point was systemic.
While they were traveling on this mission, Kristoff's memories had drudged up a connection to the Mage Underground. The plan had been that they'd tug on that connection on the way back to headquarters. See if they could use Warden privileges to build it into something bigger, into an actual grassroots revolution. But, Anders couldn't do that without Justice.
Finally, the solution came to him. Justice needed a host, and Anders had to admit to himself that he needed Justice. Mages in Thedas needed Justice.
All that was left was for both of them to consent and commit.