Temporarily Fusing Heros

First, make your "fused" Hero Battle sprites. When you come to a fight that you want the heroes to fuse at, switch in the NEW hero, and switch out the ones that fuse, make a cut-scene, showing them fusing, and there you go, fused in battle. After the battle, switch back.

This can be use to transform a hero as well, making him look different, and have him become stronger, but I recommend fusing instead, so not to give players too great of an advantage.

Now for fusing when ever you want! Start by making a plot script run before EVERY battle, asking you if you wish to fuse. If you select yes, have a text box switch on a bit set, that switches out the characters for the fusion. When the battle takes place, the fusion gets the exp instead of the main heroes. After the battles, make a plot script run that instantly switches back (as a bonus, you could have a plotscript which also awards half the experience to both of the fused heroes). If at the first plotscript, you select no, continue on as normal!