did anyone completely understand the season 1 finale? if anda did, could anda please explain the last 01-15 minutes?

ok Jones steals a plasmam thingy from nina sharp t oget to alternate universe to reconnect with william loceng meawhile walter is looking for a device to decativate the alternate universe portal in time in the end Jones dies and We find out that the original Peter is dead and died from a disease

OMG i completely understand the season finale but i think i can´t explain such a complex thing in english sorry...