The story in Countdown 2 is more or less this.
20 years ago April and his Enterprise arrived on Phaedus on a routine survey mission. They encountered an iron-age level civilization and watched a genocide in progress. The Shadows, as April's calls them, were killing (sometimes eating too) members of their own species but of different color.
At some point April had enough of watching and obeying the Prime Directive, took as many weapons as he could and beamed down to help. Alex Marcus, his first officer and best friend, agreed to declare him dead and hide the truth from Starfleet.
But it appears there was someone else now helping the Shadows and supplying them with advanced weapons. So April is hiding with the last of his native army and wants Kirk to use the Enterprise and bombard the Shadows from orbit. Kirk doesn't agree and just wants to get Sulu and Cupcake back and leave. They are prisoners of the Shadows.
The issue ends with Spock on his own. He's left Kirk without saying a word and is running towards an unknown destination.