So we still don't know

If u want spoiler, well....
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What I got from the raws was, there never had been anything between Jonathan and Kister before the whole cicero fiasco...it was all one-sided attraction from Kister tho they did met before the falling off the cliff accident...Jonathan is that type of nice guy who is oblivious that his kindness makes ppl fall for him lol
But we'll find out soon

Oh okay, if thats the case then it sounds kind of light reasoning for Cicero to want to kill Jonathan. Though he's insane so no explanation needed. Poor Jonathan, for being nice, he got involved in a psychotic family.

Thank you!!

Cicero is totally insane and psychopathic, his reasoning are not logical for us normal people...his 32 victims are said to be his father's age if the father was still alive, but I don't think other than the age they had any other similarities that warrant them to be killed....probably they just happened to slightly pissed off cicero at one point...and it looks like there will be no satisfactory explanation for this till the end..... his other motive was explained, he wanted to make Kister like him so he pushed him to kill tom march in exchange for April...
For your other question of "but why cover up for his psychotic brother" also has been explained, Kister was ridden by guilt after killing tom march that he turned himself in, also Cicero promised he wouldn't touch Jonathan anymore and that Kister thought him being in jail was punishment enough for the case...so i guess he was hoping it is finished like that...yet Cicero broke the agreement by declaring himself back, and that's when Kister knew he needed to escape prison and end all of that cuz Jonathan was once again in danger