The following article contains spoilers from Batman #130, on sale now from DC Comics.
For the last few issues of his series, Batman has been trying and failing to subdue Failsafe. In Batman #130 (by Chip Zdarsky, Jorge Jimenez, Tomeu Morey, and Clayton Cowles) he finally came up with a solution. Failsafe could not be destroyed by conventional means and Batman would need to literally change his mind. To that end, he used the small opening he created to inject a virus into Failsafe that would give the android compassion.
Unfortunately, Failsafe still completed its mission and eliminated Batman -- or so it seemed. In reality, Batman was transported to another Earth, and Failsafe then flew off without causing any more trouble. Coupling this with his assertion that what he did to Batman was compassionate, seems to suggest that Batman's plan worked. Failsafe has compassion now, and he spared Batman's life by removing him from this universe.
How Batman Made Failsafe Compassionate
Batman realized that he made Failsafe too strong, further emphasized by Failsafe beating Superman a second time. So, the only solution would be to change Failsafe's programming, making him care about human life the same way Batman does. Despite the coded compassion seemingly working, Failsafe went into the Fortress of Solitude and retrieved an unknown weapon, which he then used on Batman. Rather than killing Batman though, it merely moved him to a different Earth. This might be proof that Batman's plan worked, as Failsafe did tell a grief-stricken Tim Drake that his actions were compassionate.
When the virus took hold, Failsafe seemed to be struggling with the dual natures of his programming. One code demands he kill Batman and the other argues against taking a life. If Failsafe genuinely wanted to kill Batman, he could have done it right then and there with his bare hands. He's proven more than once that he is physically superior to Batman and in his weakened state, it would be much easier to take him out. Instead, he wandered into the Fortress and chose a specific weapon to "murder" Batman. This implies that he knew it would "eliminate" him while still honoring his newfound appreciation for life.
Batman is Far From Home
Failsafe's workaround may have spared Batman's life, but he still had to operate within the confines of his programming. It must have required Batman to have no way of coming back to interfere in the world. Death would have been the easiest solution, but now that Failsafe has turned a new leaf, he had to find a way to not cross that line. It would certainly explain why Failsafe also destroyed the device he used to remove Batman. Not only does it prevent Batman from returning, but it also stops people from being able to track him down.
However, a caption that calls this new universe a world of crime provides another possibility. Perhaps Failsafe sent Batman to a world he couldn't leave in good conscience, trusting Batman's own compassion would keep himself trapped on that planet. Another very fitting change.