A very interesting concept, especially since I'm not familiar with that particular comic. You kept the attack/abduction vague, so actually, I'm not going to ask you to remove that part. I am curious, though, what sort of gear does this Bruce even have and utilize? Without his money and resources, what tools and weaponry can I expect from this Bats?
Very reasonable question! Given Bruce can't just afford everything he'd ever desire to fight crime, he's taken the TMNT approach of mainly scavenging supplies for gadgets or jury rigging a lot of things to work. Though Donnie usually has an assortment of tools and between him and Bruce I think they can make basic stuff happen. Some of the things I've had in mind are tools the TMNT already have access to, along with some lesser-rigged bat gadgets. Some of the TMNT stuff is like the eggshell smoke bombs, which are just dried shells with a hole poked in it to drain the contents, then filled with flash powder and sealed back up with wax. Then the electricity grenades that are composed of old baseballs, batteries, and metallic rods. Without upgrades, batarangs are basically just fancy little sharp boomerangs or shurikens so I think they're fine at the end of the day. The grapple gun I didn't think was out of Bruce's reach either, as it's just a glorified grappling hook with extra durability at the end of the day, and the Turtles have had grappling hooks in the past.
Aside from that, Bruce probably still has a lock-picking set, a laser-torch (Something Donnie usually has for his own work and for utility when he needs it) and a high-intensity flashlight that is probably around 1000 lumens. *Possibly* a blow-dart gun of Donnie's design, and enough knowledge to create makeshift darts himself. And with access to flora, he can probably experiment a little and make something that's toxic or has paralyzing properties. Maybe even medicine from the wildlife, even if it's not exactly the most well-working stuff.
Bruce might start out lacking a bit, depending on how much of a prick Mojo is. As he's already been stuck in Mojoworld for a bit already, unless his equipment is gathered and/or restored after his victories, he's probably had less and less to work with unless he can also scavenge off of people he's defeated. I planned for him to do a lot of scavenging as we go along, and try to improvise with whatever he can get his hands on to help push himself further into helping the group, and achieving his own goals. So while these are just things he'd start with, He could gain a lot of new things in the future depending on where we go and what he can get his hands on reasonably.