Tia Carera (sorry, might have the wrong spelling there) was way better in Wayne's World then in this game, but hey, so what? I still have the codes. 
To jump to any point in the game go to the main menu and select GAME. Hit ALT+F5. Pick JUMP TO and it will show thumbnails of various scenes in the game. Click on one to go to it. 
To skip any puzzle hit ALT+SHIFT and the first letter of the puzzle's name, except for the Orbit puzzle. Use ALT+SHIFT+I. The code is different for each puzzle. 

Walkthrough:

======================
The Daedalus Encounter
======================

--------
Prologue
--------

Click "yes" when Ari asks you to.

When Ari asks you to deploy a probe, first click "startup", then "diagnostics",
then "deploy". As you approach the freighter, click "analysis" to ID it. To
open the door, click on the blue patch to the upper-right of the door. Click
"floodlight" when asked. Move about until Ari asks you to grab the object:
click "grapple-arm" to grab it, then click "analysis" when asked.

Click "yes" when Zack asks if you want to go to Mizar.

--------
Daedalus
--------

Immediately after the crash, click "analysis" to see the Artemis power system.
Puzzle: (each cell is represented here by a 3x3 character square) 

 
    ##############-##############
    #             |             #
    #       +-----+             #
    #       |                   #
    #       |                   #
    #       +--+                #
    #          |                #
    #          |                #
    # +--+     +--+  +--+       #
    # |  |        |  |  |       #
    # |  |       #-# |  |       #
    |-+  |     +-|#|-+  |     +-|
    #    |     | #-#    |     | #
    #    |     |  |     |     | #
    #    |  +--+  +--+  |  +--+ #
    #    |  |        |  |  |    #
    #    |  |        |  |  |    #
    # +--+  |  +-----+  +--+    #
    # |     |  |                #
    # |     |  |                #
    # +-----+  +--+             #
    #             |             #
    ##############-##############

Click "analysis" when Ari asks you to check the ship.
Deploy the probe, clicking "startup" -> "diagnostics" -> deploy".
Click "floodlight" when Ari asks.
To open the door, click any colour in the visible spectrum (you never need the
IR and UV spectrums).

-----------------------
Red Hall: Crew Quarters
-----------------------

You enter through the partially open door into the crew quarters, and cross
over to the far side. Come back to the door side. Swing right to the second
column of triads. Click on the lower triad, then on the upper-right hole.
When you're attacked, kill the alien with your laser. Click "grapple-arm" to
pick up the orb. You may have to exit and re-enter the hole, first.
Leave the quarters.

------------------------
Yellow Hall: Engine Room
------------------------

Click "analysis" on the door, translate as "246135" (i.e., the number of lines
in the alien symbol). Click the yellow light to open the door.
Puzzle:
Label the outer rotation hexes a,b,c,d,e,f, where the top-right is a
and going clockwise to the top-left f. To solve:
1) bb ccc dddd eeeee
2) bb cccc d eee fffff
3) b cc ddd eeee fffff

Click violet light at the console to open the window.
Sundial puzzle:
Label the circles 1 through 6, clockwise from lower-left to lower-right.
To solve: 1 3 5 6 2 2 6 6

Fight the krinn, and be careful not to hit Zack or Ari. When the window blows,
click violet to close the shutters. You will be injured. Click "analysis".
Probe logic circuit puzzle:
Label the switches 1 (top-right) clockwise through 9 (top-left) (i.e., the
switch with red and blue lights at the bottom is switch 5).
Solution: 3 4 1 2 6 1 4 1 2 9 2 4 1 2 5 1 2
(by switch colour: g y r b by r y r b ry b y r b rb r r)

---------------------------
Blue Hall: Hologram Chamber
---------------------------

Click "analysis" at the door, translate as "362514". Click blue to open.
Puzzle:
Label the outer rotation hexes a,b,c,d,e,f, where the top-right is "a"
and going clockwise to the top-left "f". To solve:
1) bb dddd e
2) a bbb
3) aaa bb ddd ff

To rescue the falling Zack, click thrust as soon as the indicator hits bottom,
repeating until you get to the top.

When facing the statue, click blue and see the orbit puzzle:
Four of the planets are directly movable. Call them A, B, C and D, as
they are ordered in the bottom right selection window. You must move the
fifth planet over the sun.
Solution: Move A to 11:00, C to 4:30, D to 1:20. You might need some minor
adjustments, but you do not have to move C at all.
Move to face the statue and click "send" of the "362514" code to get the orb.

---------------------------
Orange Hall: Medical Centre
---------------------------

Click "analysis" at the door, translate as "415263". Click orange to open.
Puzzle:
You must freeze the shapes into matching profiles.
Labels the figures:
b h Pair them as:
f a,l: "C"
c i b,f: large square
a l c,i: small square
d j d,j: 3/4 circle (mirror images, not exact)
g e,g: half-circle with slot in top
e k h,k: "O"

In the medical room, turn right from the door until you swing just past the
first table. Just beyond it, on the floor, is something you can close in on.
It is an orb dispenser (it looks like a colour palette / flower thingy).
"send" the "415263" code to it, and the thing above it will open and reveal an
orb. Click "grapple-arm" to pick up the orb and give it to Zack.

This time swing left from the door, past the other table. Just past the table,
up high, is a control device you can close in on. To operate it, click red,
then blue, violet, orange, and violet. It will lop off the hand of an alien.
You can't do anything with it right now.

----------------
Green Hall: Farm
----------------

Click "analysis" at the door, translate as "531642". Click green to open.
Puzzle:
Label each triangular cell by row and column: 1-1 is the top-left,
8-9 is the bottom right. The mirror positions are a for top, b for
top-right, etc. clockwise to f for top-left.
Set up mirrors in the following positions:
1) 4-7d 4-9d 2-1f 8-4f 8-5c
2) 2-6c 4-12c 5-15c 6-3c 7-7c 8-9c
3) 1-1d 1-2a 1-4e 1-9b 3-7d 3-12a 3-13b 4-7b 4-15d 5-3a 5-5a
8-3e 8-4d 8-6d 8-8b

At the farm, as you're facing the black opening, turn around and go forward
(it's a bit hard to find the spot, but it's there). You'll find another orb
dispenser. "send" it "531642" and click "grapple-arm" to get the orb.

Next time, enter the hole and click "floodlight". This is the maze:

 
            ***** 
           *     *
     +-+  +-+    *
     | |--| |    *
     +-+  +-+    *
      |    |     *
      |    |     | Corridor
     +-+  +-+   +-+   | +-+  +-+
     | | | |---| |---- | |--| |
     +-+ |+-+   +-+     +-+  +-+
      |  | |             *    |
      |  -+--          |    |
     +-+  +-+          +-+  +-+
     | |--| |   -------| |--| |
     +-+  +-+           +-+  +-+
      |                  |    |
      |                  |    |
     +-+                +-+  +-+   +-+
     | |               | |--| |--| |
     +-+               +-+  +-+   +-+
                        |    |     |
                        |    |     |
                       +-+  +-+   +-+  +-+
             ----------| |--| |   | |--| |
                        +-+  +-+   +-+  +-+
                              |     |    |
                             Farm   |    |
                                   +-+  +-+
                                   | |--| |
                                   +-+  +-+
                                    |
                                Lost Souls

Note: the maze is not entirely physical (magic at the *'s). Also, the slashes
are where the tunnels change level, and so this map shows those tunnels as
very long (and winding) to avoid overlap on the map.

--------------------
Violet Hall: Library
--------------------

Click "analysis" at the door, translate as "654321". Click violet to open.
Puzzle:
This is really a game. You must form a closed path of four or longer
before the computer does. It's not very difficult.

Close in on the panels. Each panel will show you two pictures. You have to
click various colours to make the pictures appear. Click "analysis" on each
picture, and translate each using the numeric code we've been using with
the doors.

Ari will set off a collapsing force field. "send" it "654321" to shut it off.

------
Finale
------

(You can skip the red door if you already have the orb from the crew quarters.)
Your database is full, so don't bother analysing this door. Click red to open.
Puzzle:
Label the rotation hubs a (top) clockwise through f, and g in the centre.
"a" will be a clockwise rotation, "-a" an anti-clockwise rotation.
1) -g aa -g-g -b-b g bb gg -b eee fff dd ccc ggg -c-c -g-g cc ggg d -g
2) ggg aaa -b ddd -c-c -b-b e ff eee -g-g -e-e g -d c -g-g -c -g -d-d gg dd
3) aa fff -g ee dd -g-g b -g ccc -g-g -c-c g a -g -a g f -g -f
Go to the crew quarters, kill the alien, and get the orb (see Red Hall above).

Back in the central hub, go to the yellow (2) door, click yellow to open it,
go through the next door, turn left, go through the door, and turn around.
Just to the left of the door is another orb dispenser. "send" it "246135" then
click "grapple-arm" to get the orb. Return to the hub. The orbs will be
inserted into the device.

Go to the orange door, click orange to open it, go through the next door into
the medical centre. Close in the hand you amputated earlier and click
"grapple-arm". Return to the hub.

Zack will toss the hand off. Look around on the floor and "grapple-arm" it
again.

After the elevator ride you will see a live alien. When Ari asks you to talk
to it, "send" it "452" (from one of the panels).

And they all lived happily ever after.

The End