K to beat final boss you have to prepare
1) Make sure you as fully as possible cleared all dungeons with orbs as well as in Aperture. Equipables placed there will prove little help in final battle, however you will get in fights often and thus get plenty of Exp, Gold and cheap consumables which may help. Esperally with Wheatley and Companion Cube equipped
2) Try not using consumables in battles before. Even in boss battles. You may use small medkits freely through, they are almost useless in final battle, bot don't use large medcits or revives! (you may use Crossbow to self-heal and Mana Restore skill. If any of heroes accidently die, just close game and re-load last save and try again. Save often!)
3) Before going to battle, get best equipement in C17 Mall (after or even before engaging the combine tank). Best aka giving most stats, all five equipement slots shall be replaced (most expencove equipment sold in C17 is better than anything you found before). Note that Dual Elites are have better stats than Deagle despite being cheaper! By that moment you should have plenty of money to buy all that and also consumables.
4) Useful consumables (don't remember exact names): revives (R ones, dont even tough that C revive), full health and restore, fish that restores some health and mana and Cleances, snake that restores some health and mana (if have low money). Dont buy food that only gives full mana, you can do this via spell Mana Restore (35 TP, you will often have TP for it).

So you saved at right tale (or earlier). Now go
-1) Beat Wallace Breen. Just use crits both and attack. Gabe can use Direct Hit as most powerful attack, Mike better just attack. Low health = heal with crossbow. Low mana = restore with skill (note Gabe deals more damage, better restore with Mike, luckly you can restore mana to ally). In end you should get experience enough to heall all your wounds and mana.
0) Cloaked man. Just attack him to cut his cloak
1) So you revealed Real Final Boss (RFB, won't say his real name cause of spoilers). He will fight hard, so NEVER forget you have to damage him too.
2) Most damage you can do is through Critz+Direct Hit (crit-a-cola is ineffective here and you should not have it anyway by now). Also could be fine with Poison (Mike might have one, you get one Poison skill in forest area) and Fire (both your heroes have igniting attacks), but RFB have resist to such effects. You still may try it with Mike if you got spare time (aka both have enough health Mike have enough mana).
3) So all Gabe have to do is critz and then direct hit.. in theory. But
---when critz are gone, you may want to Gabe use crossbow or restore mana to hero with less mana
---when Mike dies, you MUST revive him instantly, or next turm nay be last one for you.
---when Gave dies, he loses critz. Revive him instantly.
---when Gabe have no mana... well this should never happen, but you have to restore mana. If you have have Critz active at that time, you better use normal attack, althrough it deals less damage (you dont want to complentely waste Critz at trat moment). Always watch Gabe have enough mana
---When he have below 2500 mana and no Critz active (happens often. 2500 is ~half of all he have), he cant use Critz, so he have to go support until he have mana on Critz.
4) RFB have TONS of health and you wont see how heavily he is hutr. Dont despair. Keep attacking until he dies. At ~30% HP he will say something about 'full power' or such, but his attacks wont change. At ~10% HP another talk happens. Seems he uses only most powerful attacks after that, so focus and finish him
5) VICTORY! 1XP 1gold and illuminati staff - signs of beating Final Boss
6) enjoy the hardly achieved ending ^__^